METHOD OF DESIGNING PRIMERS, METHOD OF DETECTING SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs), METHOD OF DISTINGUISHING SNPs, AND RELATED PRIMERS, DETECTABLE OLIGONUCLEOTIDES, AND KITS

ABSTRACT

A method of designing a primer for detecting a single nucleotide polymorphism (SNP), a method of detecting an SNP, a method of distinguishing SNPs, primers, detectable oligonucleotides, and kits.

TECHNICAL FIELD

The present disclosure relates to a method of designing primers, methodsof detecting/distinguishing single nucleotide polymorphisms (SNPs),primer extension (e.g., polymerase chain reaction (PCR) and isothermalextension), peptide nucleic acids (PNAs), use of PNAs as PCR clamps,primers, detectable oligonucleotides, and kits.

BACKGROUND

Many genetic variations (including germ-line and somatic mutations) areimportant markers for hereditary abnormality, disease progression andtherapeutic efficacy. Molecular diagnostic assays based on varioustechnologies have been or are being developed to detect singlenucleotide polymorphisms (SNPs). One of the widely adopted methods isallele specific polymerase chain reaction (AS-PCR) in which allelespecific primers are designed to amplify variant specific targets basedon the selective extension by polymerase according to the 3′ matchingbetween the primer and its template. Specifically, PCR amplification isonly sufficiently effective where there are no or very few mismatchesbetween the primer and its template at or near the 3′ end of the primer,whereas PCR amplification is not detectable when the number ofmismatches at or near the 3′ end of the primer is sufficient to disrupteffective binding of the primer to the template.

The sensitivity and specificity of such methods significantly depend onthe differential PCR efficiencies between the templates containing theSNPs of interest and non-targeted templates containing other sequences,including other alleles in the case of germ-line mutations and wild-type(or other mutations) in the case of somatic mutations. When thedifference in PCR efficiency between the targeted and non-targetedtemplates is insufficient, there may be detectable amplification on thenon-targeted template (non-specific signals), and the non-specificamplification signals (e.g., Ct or signal strength), albeit lessefficient, can be too close to the specific signals (e.g., Ct or signalstrength) to fully separate low level of specific targets from thenon-specific targets. In such cases, it is difficult to establish assaycut-off to achieve both high level sensitivity and specificity. Thetechnical requirement of fully differentiated PCR efficiencies isparticularly critical in areas where very low mutant contents need to bedetected from the samples, such as many onocology-associated somaticmutations.

The BRAF gene, an example of a gene having an onocology-associatedsomatic mutation, encodes a protein belonging to the raf/mil family ofserine/threonine protein kinases (namely, serine/threonine-proteinkinase B-raf). B-raf plays a role in regulating the MAPK(mitogen-activated protein kinase) signaling pathway, which affects celldivision, cell differentiation, and secretion. Germ-line mutations inthe BRAF gene are associated with cardiofaciocutaneous syndrome, whichis characterized by heart defects, a distinctive facial appearance, andmental retardation. Mutations in the BRAF gene are also associated withvarious types of cancers, including adenocarcinoma of the lung,colorectal cancer, malignant melanoma, non-Hodgkin's lymphoma, non-smallcell lung carcinoma, and thyroid carcinoma.

Mutation of thymine at nucleotide position 1796 to adenine has beendetected in lung cancers and head and neck cancers (U.S. Pat. No.7,378,233; see U.S. Pat. No. 7,442,507 for T1799A). Detection of T1796Ain exon 15 of the BRAF gene reportedly enables a malignant papillarythyroid neoplasm to be distinguished from a benign thyroid sample (U.S.Pat. No. 7,378,233) and also enables distinction of HNPCC tumors fromsporadic colorectal tumors (Int'l Pat. App. Pub. No. WO 2005/071109).Detection of T1799A reportedly indicates the presence of metastaticmelanoma (U.S. Pat. App. No. 2006/0246476, now U.S. Pat. No. 7,442,507).

Most mutations in the BRAF gene associated with cancers occur at aminoacid position 600, which is located in the activation domain. Amino acidposition 600 also has been referred to as amino acid position 599 in theliterature. Mutation of valine (V) at amino acid position 600 toglutamic acid (E) (see, e.g., U.S. Pat. App. Pub. No. 2007/0020657,Davies, et al., Nature 417: 949-954 (2002), in which it is designatedV599E, and Kimura, et al., Cancer Res. 63: 1454-1457 (2003)), lysine(K), or aspartic acid (D) accounts for more than 90% of all mutations inthe BRAF gene. The presence of a colorectal neoplasm reportedly can bedetermined by detecting a point mutation in an exfoliated epithelialmarker, such as BRAF, along with one or more fecal occult blood markers(see U.S. Pat. App. Pub. No. 2011/0236916). Analysis of BRAF mutations,along with microsatellite stability, reportedly enables prognosis ofsurvival rates in patients with cancer as well as classification ofseverity of cancer in patients (see Int'l Pat. App. Pub. No. WO2007/009013 and U.S. Pat. App. Pub. No. 2009/0181371). See, e.g., U.S.Pat. App. Pub. No. 2011/0269124 and Int'l Pat. App. Pub. No. WO2011/019704 for detection of BRAF mutations generally. Mutation in codon599 of exon 15 of BRAF reportedly enables the detection of malignantmelanoma (see U.S. Pat. App. Pub. No. 2007/0087350; see, also, Int'lPat. App. Pub. Nos. WO 2010/097020, WO 2005/027710, WO 2005/059171, andWO 2005/066346). The use of real-time polymerase chain reaction (PCR)clamping based on peptide nucleic acid (PNA) to detect mutations incodon 600 in BRAF is described in Int'l Pat. App. Pub. No. WO2011/093606, whereas the use of allele-specific real-time quantitativePCR (AS-QPCR) using locked nucleic acid primers and beacon detectableoligonucleotides to detect V600E mutations in BRAF is described in Int'lPat. App. Pub. No. WO 2011/104694 and the use of fluorescentquantitative PCR to detect mutations in the BRAF gene is described inInt'l Pat. App. Pub. No. WO 2011/103770. Liquid chips for detecting aV600E mutation in the BRAF gene are described in Int'l Pat. App. Pub.No. WO 2011/131146. Therefore, the ability to detect single nucleotidepolymorphisms (SNPs) that lead to mutations of V600N599 would provideimportant information about the diagnosis and prognosis of cancer.

In addition to providing information about cancer diagnosis andprognosis, the ability to detect SNPs that lead to mutations ofV600/V599 also would provide important information about the therapeuticefficacy of drugs targeting the MAPK pathway. Detection of a mutation incodon 600 of BRAF, such as V600E by amplification of a polynucleotidesequence comprising V600E, reportedly enables the determination of thesensitivity of cancer cells to a B-raf kinase inhibitor (see U.S. Pat.App. Pub. Nos. 2010/0173294 and 2011/0212991). Detection ofhomozygous/heterozygous V600E or V600D genotype or any genotypecharacterized by BRAF gain-of-function phenotype reportedly enablesevaluation of sensitivity of malignant/neoplastic cells to ERK1/ERK2/MEKinhibitors (see U.S. Pat. App. Pub. No. 2011/0158944; see also Int'lPat. App. Pub. No. WO 2009/073513). The detection of a mutation in BRAF,such as V600E, reportedly enables the generation of a personalizedreport for treatment of a patient with colon cancer with cetuximab orpanitumumab (see U.S. Pat. App. Pub. No. 2011/0230360). Shinozaki, etal., Clin. Cancer Res. 13: 2068-2074 (2007), discloses the analysis ofcirculating B-RAF DNA mutations in serum for monitoring melanomapatients receiving biochemotherapy. Methods of optimizing treatment ofcancer based on BRAF mutations, as well as other methods, are describedin Int'l Pat. App. Pub. No. WO 2011/106298.

Existing methods for detecting BRAF mutations, such as sequencing,pyrosequencing, array, shifted termination assay (STA), polymerase chainreaction (PCR) followed by dual-priming oligonucleotide (DPO) PCR, andreal-time PCR utilizing either allele-specific primers orallele-specific detectable oligonucleotide are accompanied by variousdisadvantages (see, e.g., Benlloch, et al., J. Mol. Diagn. 8: 540-543(2006), for comparison of automatic sequencing and real-time chemistrymethodology in the detection of BRAF V600E mutation in colorectalcancer; see, e.g., Hay, et al., Arch. Pathol. Lab. Med. 131: 1361-1367(2007), for melting curve analysis of PCR products used to identify BRAFmutations in melanocytic lesions and papillary thyroid carcinomasamples; see, e.g., Jarry, et al., Mol. Cell. Detectableoligonucleotides 18: 349-352 (2004), for real-time allele-specificamplification in the detection of BRAF V600E; see, e.g., Sapio, et al.,Eur. J. Endocrinol. 154: 341-348 (2006), for use of mutantallele-specific PCR amplification (MASA) to detect BRAF mutation inthyroid papillary carcinoma; and, see, e.g., Turner, et al., J. Cutan.Pathol. 32: 334-339 (2005), for use of the ligase detection reaction todetect BRAF V600E in melanocytic lesions). Sequencing and pyrosequencingmethods are limited by their sensitivity, with the lowest detectablemutant content around 10-20% (% mutant over total background). Othermethods, such as real-time PCR utilizing allele-specific detectableoligonucleotides, STA, array, and PCR/DPO are also limited by theirsensitivity. Ideally, a sensitivity of 1% or better is desired.

Existing methods that lack sufficient specificity, such as real-timePCR, cannot differentiate between specific types of mutations, such asV600E and V600K. Even though V600E accounts for 90% of all mutationsfound at this amino acid position, other amino acid substitutions withclinical significant have been found in various cancers, sometimes withhigh prevalence, such as V600K in melanoma. Thus, the ability todifferentiate between specific types of mutations is becomingincreasingly important.

Assay workflow and automation are critical aspects of any diagnosticmethod. For certain technologies, such as sequencing, existing assayprocedures are long and complicated. Other technologies, such as PCR/DPO(dual priming oligo) and array-based methods, may require extensivesample handling post-PCR, which is prone to amplicon contamination. Incertain cases, additional steps have to be included in order to achievedifferentiated detection of multiple mutations.

The present disclosure seeks to overcome some of the disadvantagesattendant currently available methods of detecting germ-line and somaticmutations, especially those associated with hereditary abnormalities,disease progression and therapeutic efficacy. This and other objects andadvantages, as well as inventive features, will be apparent from thedetailed description provided herein.

SUMMARY

The present invention is that the SNPs are maintained in the context ofamino acid substitutions because it is the mutated protein that isdirectly involved in the biological abnormality. Another insight is thatthe SNPs themselves are directly involved in the process of generegulation, such as disruption of a splicing event. It is also possiblethat some of the SNPs have no obvious or known impact on biologicalfunctions but are co-localized with the SNPs of interest in the primarynucleotide sequence.

Thus, the present invention is directed towards compositions and methodssuitable for the improved detection of SNPs (i.e., target SNPs). Theimproved detection of SNPs afforded by the present invention is based onthe novel and non-obvious discovery of a new approach to primer design.The primer designs suitable for the detection of SNPs (as discussed,infra) are summarized in FIGS. 2 and 3. It is noted here that the commonfeature to all designs is the introduction of one or more additionalmismatched bases 5′ to the naturally occurring mismatches to allow forallele specific priming. The rationale for this design feature is asfollows: The naturally occurring mismatches can sometimes be toleratedby polymerase depending upon the content, number and position(s) of themismatch(es). The introduced additional mismatch(es) are designed tofurther reduce PCR efficiency for the non-specific targets withoutsignificantly impacting the specific targets. As a result, the targetswith the mutations of interest will be amplified efficiently whilenon-specific targets will not due to the presence of 2 or moremismatched at or near the 3′ end of the primers. This design feature canbe applied to either the forward or reverse primer to enable the allelespecific priming. As described in FIGS. 2 and 3, such a design mayalready be sufficient to achieve allele specific detection and/oridentification. Depending on the actual SNP pattern, e.g., in caseswhere two individual SNPs are far apart, it may be feasible to detectspecific SNPs if both the forward and reverse primers are designed to beallele specific (see, FIG. 5). In addition to the SNPs of interest,there might be other existing SNPs nearby that are not clinicallyrelevant and need to be tolerated by the assay. One solution is todesign degenerate bases at those positions (see, FIG. 2, example 2) orother modified nucleotide bases allowing indiscriminate binding.

The design principles and strategies described above and exemplifiedbelow can be adopted for use with codon-based AS-PCR to detect singleamino acid mutations. In the genetic codon table, every amino acidincluding the stop codon (TGA/UGA) is encoded by a different array ofthree nucleotides. In order to minimize non-specific signals from otheramino acid mutations and/or nominal sequences that can potentially bepresent in a sample, the SNPs region for the whole codon need to beincluded in the primer design. In order to detect multiple codonscorresponding to one amino acid mutation of interest (depending on thespecific amino acid) or multiple amino acid mutations, multiple allelespecific primers are used (as a pool or separately), each carrying a 3′end sequence that is specific to one of the codons of interest. Theseallele specific primers have a perfect match with their intended targetsat the last 3 nucleotides of the 3′ terminus but will have at least onemismatch in the same region when compared with any other codon. Asdiscussed above, one mismatch among the last 3 nucleotides of a primercan sometimes by tolerated by the polymerase; hence one additionalmismatch in introduced at a nucleotide position 5′ to the codons ofinterest to further reduce PCR efficiency for the no-specific targetwithout significantly impacting the specific targets. As a result, thetargets with only the amino acid mutations of interest will be amplifieswhile other non-specific target(s) will not due to the presence of 2 ormore mismatches at or near the 3′ end of the primer. This strategy notonly covers all possible genetic variations that encode the amino acidof interest but also eliminates the non-specific signals from all otherpotential amino acids (from either mutated or wild-type sequences).

One of ordinary skill in the art would, from the teachings of thepresent specification, be able to design primers for use in SNPdetection for any desired target. One exemplification below teaches amethod of detecting at least one mutation (X) of the codon encodingvaline at amino acid position 600 (V600X) in exon 15 of the BRAF gene ina sample of nucleic acid from a human is provided. The method comprises:

(a) performing an amplification reaction with the sample of nucleicacid, wherein the amplification reaction comprises a primer, the lastthree nucleotides at the 3′ terminus of which encodes X and wherein thefourth nucleotide from the 3′ terminus contains a base other thanadenine (A), wherein, if X is present, the primer anneals to x,

wherein, if the sample of nucleic acid is mRNA, step (a) furthercomprises obtaining cDNA reverse-transcribed from the mRNA orreverse-transcribing cDNA from the mRNA before performing theamplification reaction,

whereupon, if X is present, the amplification reaction produces anamplification product comprising X,

(b) detecting the amplification product comprising X, and

wherein, if X is encoded by more than one codon, the amplificationreaction comprises a primer for each codon. The amplification reactioncan further comprise at least one peptide nucleic acid (PNA) clamp,wherein at least one PNA clamp is wild-type and, if the amplificationreaction comprises one or more other PNA clamps, the PNA clamps adetectable oligonucleotide and/or a primer, the PNA clamps a detectableoligonucleotide and/or a primer by binding an unwanted target andpreventing a primer from amplifying from an unwanted target. Detectingthe amplification product comprising X can comprise detecting a labeledprimer or contacting the amplification product with a detectableoligonucleotide and detecting hybridization of the detectableoligonucleotide to the amplification product comprising X. Theamplification reaction can further comprise an internal control primer,in which case the amplification reaction also produces an amplificationproduct comprising the internal control, in which case step (b) includesdetecting the amplification product comprising the internal control.Detecting the amplification product comprising the internal control cancomprise detecting a labeled primer or contacting the amplificationproduct with a detectable oligonucleotide and detecting hybridization ofthe detectable oligonucleotide to the amplification product comprisingthe internal control. X is at least one amino acid selected from thegroup consisting of E, K, D, R, and N. For example, X can be at leastone amino acid selected from the group consisting of E, K, and D. X canbe E, E and K, E and D, K and D, or E, K, and D. When the methodcomprises detecting two or more X, the method can comprise performing anamplification reaction with the sample of DNA for each X together orseparately. In this regard, the method also can further comprisedetermining which X is present in the sample of nucleic acid.

The present invention is also directed to set of primers foramplification of

V600X in exon 15 of the BRAF gene in a sample of nucleic acid from ahuman is also provided. The set of primers comprises at least one primerselected from the group consisting of:

(a) an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACNGAA [SEQ ID NO: 44] at its 3′ terminus and/or anoligonucleotide comprising the nucleotide sequence GGTCTAGCTACNGAG [SEQID NO: 45] at its 3′ terminus,

(b) an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACNAAA [SEQ ID NO: 46] at its 3′ terminus and/or anoligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAG [SEQID NO: 47] at its 3′ terminus,

(c) an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACNGAT [SEQ ID NO: 48] at its 3′ terminus and/or anoligonucleotide comprising the nucleotide sequence GGTCTAGCTACNGAC [SEQID NO: 49] at its 3′ terminus,

(d) an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACNAAT [SEQ ID NO: 50] at its 3′ terminus and/or anoligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAC [SEQID NO: 51] at its 3′ terminus,

(e) an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACNCGT [SEQ ID NO: 52] at its 3′ terminus, an oligonucleotidecomprising the nucleotide sequence GGTCTAGCTACNCGC [SEQ ID NO: 53] atits 3′ terminus, an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACNCGA [SEQ ID NO: 54] at its 3′ terminus, an oligonucleotidecomprising the nucleotide sequence GGTCTAGCTACNCGG [SEQ ID NO: 55] atits 3′ terminus, an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACN AGA [SEQ ID NO: 56] at its 3′ terminus, and anoligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAGG [SEQID NO: 57] at its 3′ terminus,

(d) and (e),

(a) and (b),

(a) and (c),

(b) and (c),

(a), (b), and (c),

any of (a), (b), and (c), in further combination with (d),

any of (a), (b), and (c), in further combination with (e), and

any of (a), (b), and (c), in further combination with (d) and (e),

wherein N is a nucleotide containing a base other than adenine (A), and

wherein the oligonucleotide comprises from about 15 nucleotides to about35 nucleotides. The oligonucleotide can further comprise contiguous withthe G at the 5′ end of the nucleotide sequence one or more contiguousnucleotides of the nucleotide sequence 5′ AATAGGTGATTTT 3′ [SEQ ID NO:58] starting with the Tat the 3′ end of the nucleotide sequence. The setof primers can further comprise a primer, such as a reverse primer,comprising from about 15 nucleotides to about 35 nucleotides, wherein,when the primer comprises 15-27 nucleotides, it comprises 15-27contiguous nucleotides of SEQ ID NO: 10. The detectable oligonucleotidecan comprise from about 15 nucleotides to about 35 nucleotides, wherein,when the detectable oligonucleotide comprises 15-20 nucleotides, itcomprises 15-20 contiguous nucleotides of SEQ ID NO: 11.

A kit is also provided. The kit comprises:

(i) a set of primers for detection of V600X in exon 15 of the BRAF genein a sample of nucleic acid from a human, wherein the set of primerscomprises at least one primer selected from the group consisting of:

-   -   (a) an oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNGAA [SEQ ID NO: 44] at its 3′ terminus and/or an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNGAG [SEQ ID NO: 45] at its 3′ terminus,    -   (b) an oligonucleotide comprising the nucleotide sequence

GGTCTAGCTACNAAA [SEQ ID NO: 46] at its 3′ terminus and/or anoligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAG [SEQID NO: 47] at its 3′ terminus,

-   -   (c) an oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNGAT [SEQ ID NO: 48] at its 3′ terminus and/or an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNGAC [SEQ ID NO: 49] at its 3′ terminus,    -   (d) an oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNAAT [SEQ ID NO: 50] at its 3′ terminus and/or an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNAAC [SEQ ID NO: 51] at its 3′ terminus,    -   (e) an oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNCGT [SEQ ID NO: 52] at its 3′ terminus, an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNCGC [SEQ ID NO: 53] at its 3′ terminus, an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNCGA [SEQ ID NO: 54] at its 3′ terminus, an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNCGG [SEQ ID NO: 55] at its 3′ terminus, an        oligonucleotide comprising the nucleotide sequence GGTCTAGCTACN        AGA [SEQ ID NO: 56] at its 3′ terminus, and an oligonucleotide        comprising the nucleotide sequence GGTCTAGCTACNAGG [SEQ ID NO:        57] at its 3′ terminus,    -   (d) and (e),    -   (a) and (b),    -   (a) and (c),    -   (b) and (c),    -   (a), (b), and (c),    -   any of (a), (b), and (c), in further combination with (d),    -   any of (a), (b), and (c), in further combination with (e), and    -   any of (a), (b), and (c), in further combination with (d) and        (e),

wherein N is a nucleotide containing a base other than adenine (A), and

wherein the oligonucleotide comprises from about 15 nucleotides to about35 nucleotides, and

(ii) instructions for a method of detecting at least one mutation (X) ofthe codon encoding valine at amino acid position 600 (V600X) in exon 15of the BRAF gene in a sample of nucleic acid from a human, which methodcomprises:

(a) performing an amplification reaction with the sample of nucleicacid, wherein the amplification reaction comprises a primer, the lastthree nucleotides at the 3′ terminus of which encodes X and wherein thefourth nucleotide from the 3′ terminus contains a base other thanadenine (A), wherein, if X is present, the primer anneals to X, and atleast one peptide nucleic acid (PNA) clamp, wherein at least one PNAclamp blocks the amplification from wild-type target,

wherein, if the sample of nucleic acid is mRNA, step (a) furthercomprises obtaining cDNA reverse-transcribed from the mRNA orreverse-transcribing cDNA from the mRNA before performing theamplification reaction,

whereupon, if X is present, the amplification reaction produces anamplification product comprising X, and

(b) detecting the amplification product comprising X,

wherein, if X is encoded by more than one codon, the amplificationreaction comprises a primer for each codon,

wherein, if the method comprises detecting two or more X, the method cancomprise performing an amplification reaction with the sample of nucleicacid for each X together or separately, and

wherein the method also can further comprise determining which X ispresent in the sample of nucleic acid. The oligonucleotide can furthercomprise contiguous with the G at the 5′ end of the nucleotide sequenceone or more contiguous nucleotides of the nucleotide sequence 5′AATAGGTGATTTT 3′ [SEQ ID NO: 58] starting with the T at the 3′ end ofthe nucleotide sequence. The kit can further comprise a primer, such asa reverse primer, comprising from about 15 nucleotides to about 35nucleotides, wherein, when the primer comprises 15-27 nucleotides, itcomprises 15-27 contiguous nucleotides of SEQ ID NO: 10. The kit canfurther comprise a detectable oligonucleotide comprising from about 15nucleotides to about 35 nucleotides, wherein, when the detectableoligonucleotide comprises 15-20 nucleotides, it comprises 15-20contiguous nucleotides of SEQ ID NO: 11. X can be at least one aminoacid selected from the group consisting of E, K, D, R, and N. X can beat least one amino acid selected from the group consisting of E, K, andD, such as E, E and K, E and D, K and D, or E, K, and D.

The present invention is not limited to the detection of BRAF mutationsand one of ordinary skill in the art, based on the teachings of thepresent specification, would be able to design primers and assays forthe detection of any desired target SNP. Thus, the present invention isalso directed towards a method of detecting at least one mutation (X) ofa codon in a gene in a sample of nucleic acid is also provided. Themethod comprises:

(a) performing an amplification reaction with the sample of nucleicacid, wherein the amplification reaction comprises a primer, the lastthree nucleotides at the 3′ terminus of which encodes X and wherein thefourth nucleotide from the 3′ terminus contains a base other thanadenine (A), wherein, if X is present, the primer anneals to X,

wherein, if the sample of nucleic acid is mRNA, step (a) furthercomprises obtaining cDNA reverse-transcribed from the mRNA orreverse-transcribing cDNA from the mRNA before performing theamplification reaction,

whereupon, if X is present, the amplification reaction produces anamplification product comprising X,

(b) detecting the amplification product comprising X, and

wherein, if X is encoded by more than one codon, the amplificationreaction comprises a primer for each codon. The amplification reactioncan further comprise at least one peptide nucleic acid (PNA) clamp,wherein at least one PNA clamp blocks the amplification from wild-typetarget, and wherein, if the amplification reaction comprises one or moreother PNA clamps, the PNA preferably clamps a detectable oligonucleotideand/or a primer. Detecting the amplification product comprising X cancomprise detecting a labeled primer or contacting the amplificationproduct with a detectable oligonucleotide and detecting hybridization ofthe detectable oligonucleotide to the amplification product comprisingX. The amplification reaction can further comprise an internal controlprimer, in which case the amplification reaction also produces anamplification product comprising the internal control, in which casestep (b) includes detecting the amplification product comprising theinternal control. Detecting the amplification product comprising theinternal control can comprise detecting a labeled primer or contactingthe amplification product with a detectable oligonucleotide anddetecting hybridization of the detectable oligonucleotide to theamplification product comprising the internal control. When the methodcomprises detecting two or more X, the method can comprise performing anamplification reaction with the sample of nucleic acid for each Xtogether or separately. In this regard, the method also can furthercomprise determining which X is present in the sample of nucleic acid.

A method of designing a primer for detection of at least one mutation(X) of a codon in a gene in a sample of nucleic acid is also provided.The method comprises synthesizing a primer, the last three nucleotidesat the 3′ terminus of which encodes X and wherein the fourth nucleotidefrom the 3′ terminus contains a base other than that which is present inthe wild-type gene, whereupon a primer for detection of at least onemutation (X) in a codon in a gene in a sample of nucleic acid isdesigned.

The present invention is also directed towards a dual allele specificprimer design strategy. In situations where there are multiple SNPs ofinterest in multiple positions, with one SNP per position, for example,the simultaneous presence of multiple SNPs in a given sample will bedetected. The single SNP should not be detected. An exemplification ofthe dual allele specific primer design strategy is given in FIG. 5. Inthis regard, the primer design exemplified in FIG. 2 can be applied toeither the forward or the reverse primer in the dual allele specificprimer design method of the present invention.

The present invention also contemplates a method for detecting asequence of nucleic acid comprising a target single nucleotidepolymorphism (SNP) of interest (the first SNP of interest), said methodcomprising: a) providing i) a sequence of nucleic acid suspected ofcontaining the target SNP, ii) a primer that is complementary to thesequence comprising the target SNP, wherein the base located three bases5′ from a primer nucleotide that is complementary to the target SNP is abase that is not complementary to the corresponding base of the nucleicacid comprising the target SNP sequence, thereby creating in the primera mismatched base; b) contacting the sample suspected of containing thetarget SNP with the primer under conditions that permit the binding ofthe primer to the target SNP, if present, to create a bound target SNP;and c) detecting the bound target SNP. The present invention alsocontemplates that wherein if the sample of nucleic acid is mRNA, step b)further comprises obtaining cDNA reverse-transcribed from the mRNA orreverse-transcribing cDNA from the mRNA.

The present invention also contemplates that when the sequence ofnucleic acid comprises more than one SNP (the second SNP of interest), aseparate primer is used to detect the second SNP of interest.

The present invention also contemplates that when the sequence ofnucleic acid comprising the target SNP of interest comprises one or morenon-target mutations, the primer contains nucleotides complementary tosaid one or more non-target mutations.

The present invention also contemplates that when the sequence ofnucleic acid comprising the target SNP of interest (the first SNP ofinterest) contains one or more additional target SNPs of interest at thesame sequence position that the method additionally comprises a primercontaining a base complementary to each additional one or more SNPs ofinterest.

The present invention also contemplates that when the sequence ofnucleic acid comprising the target SNP of interest (the first SNP ofinterest) contains one or more additional target SNPs of interest at asequence location or locations that differ from the sequence location ofthe first SNP of interest, the primer additionally comprises a base orbases complementary to the one of more additional SNPs of interest.

The present invention also contemplates a method for detecting asequence of nucleic acid comprising one or more target single nucleotidepolymorphisms (SNP) of interest, wherein the SNPs are located at one ormore positions on the sequence of nucleic acid, the method comprising:a) providing, i) a sequence of nucleic acid suspected of containing theone or more target SNPs such that the first sequence containing one ormore SNPs is the first sequence and such that the most 5′ SNP is thefirst target SNP, a second sequence containing one of more SNPs whereinat least one SNP differs from the one or more SNPs of the firstsequence, is the second sequence and such that the most 5′ SNP is thefirst target SNP, etc., ii) a primer complementary to each sequencecomprising the one or more target SNPs wherein for each primer the baselocated three bases 5′ from a primer nucleotide that is complementary tothe first target SNP is a base that is not complementary to thecorresponding base of the nucleic acid comprising the target SNPsequence, thereby creating in the primer a first mismatched base; b)contacting the sample suspected of containing the sequences containingthe one or more target SNPs with the primer or primers under conditionsthat permit the binding of the primer or primers to the one or moretarget SNPs, if present, to create a bound target SNPs; and c) detectingthe bound target SNPs. The present invention also contemplates thatwherein if the sample of nucleic acid is mRNA, step b) further comprisesobtaining cDNA reverse-transcribed from the mRNA or reverse-transcribingcDNA from the mRNA.

The present invention also contemplates a dual allele specific primerstrategy (see, FIG. 5) wherein both forward and reverse primers arecreated for the detection of multiple target SNPs in a nucleotidesequence.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 illustrates the design of primers, wherein the V600 codon isunderlined.

FIG. 2 shows multiple primer design strategies of the present invention.

FIG. 3 shows a schematic diagram illustrating the design principle foramino acid specific primers using BRAF V600E as a model target.

FIG. 4 shows amino acid specific primer design for BRAF V600E as a modeltarget.

FIG. 5 shows the dual allele specific primer design strategy of thepresent invention.

FIGS. 6 A & B show a comparison of two different primer designs for BRAFV600E detection. Also shown are the number of mismatched bases in eachprimer design.

FIG. 7 A & B show a comparison of two different primer designs for BRAFV600E detection presented as (A) CT and (B) PCR curves.

FIG. 8 shows the results of SNP detection using primers specific foreither V600E or V600K.

DETAILED DESCRIPTION

The present disclosure is predicated, at least in part, onoligonucleotide primers and detectable oligonucleotides for thereal-time amplification and detection of a single or multiple nucleotidepolymorphisms (SNP). The detection of the SNP at amino acid position 600of BRAF is an example. This SNP can result in substitution of valinewith glutamic acid (designated herein as V600E), lysine (designatedherein as V600K), aspartic acid (V600D), arginine (V600R), or asparagine(V600N), for example. Since mutation of valine at amino acid position600 to glutamic acid, lysine, and/or aspartic acid accounts for morethan 90% of all BRAF mutations, the primers and detectableoligonucleotides provided herein enable, among other things, cancerprognosis and assessment of therapeutic efficacy of a drug targeting theMAPK pathway.

Allele-specific amplification and polymerase chain reaction (PCR)clamping are combined to detect the SNP. The combination enablessensitivity lower than or equal to about 0.5% mutant content withexcellent specificity.

The following definitions are relevant to the present disclosure:

(a) “About” refers to approximately a +/−10% variation from the statedvalue. It is to be understood that such a variation is always includedin any given value provided herein, whether or not specific reference ismade to it.

(b) “Allele-specific primer” in the context of the present disclosurerefers to a primer (see “primer”) that hybridizes to a target sequencesuch that the 3′ end, usually the 3′ nucleotide, of the primer alignswith a site of interest, e.g., nucleotide 1800, which is the thirdnucleotide in codon 600 of BRAF, and is exactly complementary to eitherthe wild-type allele or a mutant allele at the codon of the SNP. The useof an allele-specific primer enables discrimination between allelesbased on differential formation of extension products during nucleicacid, e.g., DNA, amplification.

(c) “Detectable oligonucleotide” refers to an oligonucleotide thatselectively hybridizes to a target nucleic acid under suitableconditions and can be detected.

(d) “High-affinity nucleic acid analogue” refers to a modified nucleicacid that hybridizes to a complementary nucleic acid, such as adeoxyribonucleic acid (DNA), with higher affinity than an unmodifiednucleic acid having the same base sequence. High-affinity nucleic acidsinclude, but are not limited to, locked nucleic acids (LNAs), peptidenucleic acids (PNAs), hexitol nucleic acids (HNAs), phosphoramidates,and the like.

(e) “Hybridization” refers to the formation of a duplex structure bycomplementary base pairing between two single-stranded nucleic acids.Hybridization can occur between exactly complementary nucleic acidstrands or between complementary nucleic acid strands that contain a lownumber of mismatches.

(f) “Locked nucleic acid (LNA)” refers to a nucleic acid analogue (apolymer of purine and/or pyrmidine bases) characterized by the presenceof one or more monomers that are conformationally restricted nucleotideanalogues with an extra 2H—O, 4H—C-methylene bridge added to the ribosering. LNA has been defined as an oligonucleotide having one or more2H—O, 4H—C-methylene-(D-ribofuranosyl)nucleotide monomers. LNAs areresistant to exonucleases and heat.

(g) “Nucleic acid,” “polynucleotide,” and “oligonucleotide” refer toprimers, detectable oligonucleotides, and oligomers, irrespective oflength, and include polydeoxyribonucleotides, polyribonucleotides, andany other N-glycoside of a modified/unmodified, purine/pyrmidine base.Examples include single-stranded DNA (ssDNA), double-stranded DNA(dsDNA), single-stranded RNA (ssRNA), and double-stranded RNA (dsRNA).Such molecules can comprise phosphodiester linkages or modified linkagesincluding, but not limited to, phosphotriester, phosphoramidate,siloxane, carbonate, carboxymethylester, acetamidate, carbamate,thioether, bridged phosphoramidate, bridged methylene phosphonate,phosphorothioate, methylphosphonate, phosphorodithioate, bridgedphosphorothioate or sulfone linkages, and combinations thereof. Suchmolecules can comprise adenine, guanine, thymine, cytosine and/oruracil, as well as other modified, non-standard, or derivatized bases.Alternatively or additionally, such molecules can comprise one or moremodified sugar moieties.

(h) “Peptide nucleic acid (PNA)” refers to a synthetic DNA analog inwhich the normal phosphodiester backbone is replaced with aN-(2-aminoethyl)glycine chain. Its nucleobases complement DNA or RNA inthe same A-T(U) and G-C manner (Nielsen, et al., Science 254: 1497-1500(1991); Hanvey, et al., Science 258: 1481-1485 (1992); and Egholm, etal., Nature 365: 566-568 (1993)). The artificial backbone renders PNAresistant to nucleases. PNA can be synthesized in accordance withmethods known in the art (see, e.g., Hyrup, et al., Bioorg. Med. Chem.4: 5-23 (1996); Int'l Pat. App. Pub. Nos. WO 92/20702 and 92/20703; andU.S. Pat. No. 5,539,082, the contents of all of which are incorporatedherein by reference for their teachings regarding same). Two importantfeatures make PNA a superior PCR clamp for specific alleles. It cannotserve as a primer for polymerization. It cannot serve as a substrate forexonuclease activity by Taq polymerase. In addition, the meltingtemperature of a perfectly matched PNA-DNA duplex is higher than that ofa DNA-DNA duplex of the same length; thus, the PNA-DNA duplex is morestable. A single mismatch in a PNA-DNA hybrid will cause a drop in themelting temperature of about 10-18° C. (Kyger, et al., Anal. Biochem.260: 142-148 (1998)). Therefore, over an appropriate temperature rangePNA can specifically block primer/detectable oligonucleotide annealingor chain elongation on a perfectly matched template without interferingwith reactions on templates with mismatched base(s) (Sun, et al., Nat.Biotechnol. 20: 186-189 (2002); Thiede, et al., Nucleic Acids Res. 24:983-984 (1996); and Taback, et al., Int. J. Cancer 111: 409-414 (2004)),which is referred to as PNA-mediated PCR clamping (Orum, et al., NucleicAcids Res. 21: 5332-5336 (1993)). The large difference in meltingtemperature between perfectly matched and mismatched hybrids makes PNA agood sensor of point mutations (see, e.g., Karadag, et al., NucleicAcids Res. 32: e63 (2004); Taback, et al. (2004), supra; Hancock, etal., Clin. Chem. 48: 2155-2163 (2002); Takiya, et al., Biosci.Biotechnol. Biochem. 68: 360-368 (2004); Kirishima, et al., J. Hepatol.37: 259-265 (2002); and Ohishi, et al., J. Med. Virol. 72: 558-565(2004)). U.S. Pat. App. Pub. No. 2004/0014105 discloses methods for theselective enrichment of polynucleotides that are present in a sample inlow abundance. The method uses enzymatically non-extendable nucleobaseoligomer (e.g., PNA) as a PCR clamp to block selectively polymeraseactivity on polynucleotides that are present in the sample in highabundance, thereby resulting in an enrichment of less abundant speciesin the sample. “PNA” may include a PNA clamp. Clamping operates byphysical competition between a PNA and a DNA primer or probe for acommon target site, thereby interfering with primer elongation.

(i) “Polymerase chain reaction (PCR)” is a method of making copies of aDNA sequence. The method employs thermal cycling (i.e., cycles ofheating and cooling for denaturation (or melting) and replication of theDNA, respectively). Primers, which are short DNA fragments containingsequences complementary to the DNA sequence to be copied, and aheat-stable DNA polymerase, such as the one from Thermus aquaticus,which is referred to as Taq polymerase, are used to select the DNAsequence and copy it (see, e.g., U.S. Pat. Nos. 4,683,195; 4,800,195,and 4,965,188, all of which are incorporated by reference herein fortheir teachings regarding same). With repeated cycling the copies, whichare made, are used as templates for generating further copies (i.e., achain reaction). PCR techniques include, but are not limited to,standard PCR, allele-specific PCR, assembly PCR, asymmetric PCR, digitalPCR, Hot-start PCR, intersequence-specific PCR, inverse PCR,ligation-mediated PCR, methylation-specific PCR, mini-primer PCR, nestedPCR, overlap-extension PCR, real-time PCR, reverse transcription-PCR,solid phase PCR, thermal asymmetric interlaced PCR, and Touchdown PCR.

(j) “Primer” as used herein refers to an oligonucleotide that initiatestemplate-dependent nucleic acid synthesis. In the presence of a nucleicacid template, nucleoside triphosphate precursors, a polymerase, andcofactors, under suitable conditions of temperature and pH, the primercan be extended at its 3′ terminus by the addition of nucleotides by thepolymerase to yield a primer extension product. The primer may vary inlength depending on the particular conditions employed and the purposeof the amplification. For example, a primer for amplification for adiagnostic purpose is typically from about 15 to about 35 nucleotides inlength. The primer must be of sufficient complementarity to the desiredtemplate to prime the synthesis of the desired extension product. Inother words, the primer must be able to anneal with the desired templatestrand in a manner sufficient to provide the 3′ hydroxyl moiety of theprimer in appropriate juxtaposition for use in the initiation ofsynthesis by a polymerase. It is not necessary for the primer to be anexact complement of the desired template. For example, anon-complementary nucleotide sequence can be present at the 5′ end of anotherwise complementary primer. Alternatively, non-complementary basescan be interspersed within the oligonucleotide primer, provided that theprimer sequence has sufficient complementarity with the sequence of thedesired template strand to provide a template-primer complex for thesynthesis of the extension product.

(k) “Specifically hybridize(s),” as used herein, refers to the abilityof a given nucleic acid, such as a primer or detectable oligonucleotide,to bind specifically to another nucleic acid.

(l) “Stringent” or “sequence-specific” hybridization conditions refersto conditions under which exactly complementary nucleic acid strand willpreferentially hybridize. Stringent hybridization conditions arewell-known in the art. Stringent conditions are sequence-dependent andwill be different under different circumstances. Generally, stringentconditions are selected to be about 5° C. lower than the thermal meltingpoint (T_(m)) for the specific sequence under defined conditions of pHand ionic strength at which 50% of the base pairs are dissociated.

(m) “Substantially complementary” refers to sequences that arecomplementary except for minor regions of mismatches. Typically, thetotal number of mismatches in a nucleic acid that is about 15nucleotides in length is about 3 nucleotides or less.

(n) “Target sequence” and “target region” refer to a region of a nucleicacid that it to be detected, or detected and analyzed, and comprises thepolymorphic site of interest, i.e., V600D, V600E, V600K, V600N, or V600Rin the context of the present disclosure.

(o) “V600D” refers to a TG→AT or TG→AC mutation starting at nucleotideposition 1799 of BRAF that results in substitution of aspartic acid forvaline.

(p) “V600E” refers to a T→A or TG→AA mutation starting at nucleotideposition 1799 of BRAF that results in substitution of glutamic acid forvaline. V600E is also known as V599E (T→A mutation at nucleotideposition 1796 of BRAF) under a previous numbering system (Kumar, et al.,Clin. Cancer Res. 9: 3362-3368 (2003)).

(q) “V600K” refers to a GT→AA or GTG→AAA mutation starting at nucleotideposition 1798 of BRAF that results in substitution of lysine for valine.

(r) “V600N” refers to a GTG→AAT or GTG→AAC mutation starting atnucleotide position 1798 of BRAF that results in substitution ofasparagine for valine.

(s) “V600R” refers to a GT→AG, GT→CG, GTG→AGA, GTG→CGT, GTG→CGC, orGTG→CGA mutation starting at nucleotide position 1798 of BRAF thatresults in substitution of arginine for valine.

The terminology used herein is for the purpose of describing particularembodiments only and is not otherwise intended to be limiting.

Method of Detection

A method of detecting at least one mutation (X) of the codon encoding,for example, valine at amino acid position 600 (V600X) in exon 15 of theBRAF gene, in a sample of nucleic acid from a subject (e.g., a humansubject) is provided. The method comprises:

(a) performing an amplification reaction with the sample of nucleicacid, wherein the amplification reaction comprises a primer, the lastthree nucleotides at the 3′ terminus of which encodes X and wherein thefourth nucleotide from the 3′ terminus contains a base other thanadenine (A), wherein, if X is present, the primer anneals to x,

wherein, if the sample of nucleic acid is mRNA, step (a) furthercomprises obtaining cDNA reverse-transcribed from the mRNA orreverse-transcribing cDNA from the mRNA before performing theamplification reaction,

whereupon, if X is present, the amplification reaction produces anamplification product comprising X,

(b) detecting the amplification product comprising X, and wherein, if Xis encoded by more than one codon, the amplification reaction comprisesa primer for each codon. With regard to a primer, reference is madeherein to the nucleotides (nt) at the 3′ terminus as follows:

nt -- nt -- nt -- nt 3′ Position: 4th 3rd 2nd 1st.The amplification reaction can further comprise at least one peptidenucleic acid (PNA) clamp, wherein at least one PNA clamp blocks theamplification from wild-type target, and wherein, if the amplificationreaction comprises one or more other PNA clamps, the PNA preferablyclamps a detectable oligonucleotide and/or a primer by binding anunwanted target and prevents a primer from amplifying from an unwantedtarget. Detecting the amplification product comprising X can comprisedetecting a labeled primer or contacting the amplification product witha detectable oligonucleotide and detecting hybridization of thedetectable oligonucleotide to the amplification product comprising X.The amplification reaction can further comprise an internal controlprimer, in which case the amplification reaction also produces anamplification product comprising the internal control, in which casestep (b) includes detecting the amplification product comprising theinternal control. Detecting the amplification product comprising theinternal control can comprise detecting a labeled primer or contactingthe amplification product with a detectable oligonucleotide anddetecting hybridization of the detectable oligonucleotide to theamplification product comprising the internal control. X is at least oneamino acid selected from the group consisting of E, K, D, R, and N. Forexample, X can be at least one amino acid selected from the groupconsisting of E, K, and D. X can be E, E and K, E and D, K and D, or E,K, and D. X also can be another amino acid besides E, K, D, R, or N,including V encoded by a codon other than that which is found inwild-type (i.e., a silent mutation), or a premature stop codon.Preferably, however, X is at least one of E, K, D, R, or N as indicated.

When the method comprises detecting two or more X, the method cancomprise performing an amplification reaction with the sample of nucleicacid for each X together or separately. In this regard, the method alsocan further comprise determining which X is present in the sample ofnucleic acid.

The amplification reaction can, and preferably does, comprise aninternal control (IC) nucleic acid and a pair of primers for amplifyingthe IC nucleic acid. When the amplification reaction comprises an ICnucleic acid, the conditions that promote amplification also promoteamplification of the IC nucleic acid.

Thus, primer selection enables detection of at least one mutation inaccordance with the present disclosure. This is in distinct contrast tomethods of the prior art in which detectable oligonucleotide selectionenables detection of a mutation. The present method is also specific formutation at the amino acid level (i.e., primers are selected to amplifyall codons encoding a particular amino acid but no other amino acid).This is in distinct contrast to methods of the prior art, which arespecific for nucleic acids and detect multiple amino acids encoded bycodons in which the nucleotides at the first and second positions of thecodon are the same. Furthermore, the present method can be performed onDNA or RNA, is inherently quantitative, and can be adapted for detectionof SNPs in other locations in the same gene as well as SNPs in othergenes.

Any suitable sample of a tissue or a body fluid can be used as thesource of the sample of nucleic acid, i.e., DNA or RNA. Typically, thesource is a tumor or cells/tissues from a metastatic site or blood (orcomponent thereof). Blood, plasma, serum, lymph, and tumor biopsies, forexample, can be used. Other samples include urine, cerebrospinal fluid,pleural fluid, sputum, peritoneal fluid, bladder washings, secretions(e.g., breast), oral washings, touch preparations, and fine-needleaspirates. A plasma or whole blood can be preserved, such as by theaddition of a chelating agent, e.g., ethylenediaminetetraacetic acid(EDTA) or a salt thereof, such as a disodium salt or a calcium disodiumsalt. A proteinase, such as proteinase K, can be added to the sample todigest unwanted proteins.

Tissue samples can be generally preserved as formalin-fixed,paraffin-embedded (FFPE) blocks. Tissue sections of varying thickness,such as 5μm, are cut from such tissue blocks and either left unmountedor mounted onto a solid support, such as a slide, by standard means. Thecellular morphology of the tissue sample is revealed using a variety offixatives and/or stains and visualized microscopically. If the densityof cells, such as cancer cells, e.g., melanoma cells, in a tissue sampleis sufficient (greater than about 1%), the section is scraped from theslide, and DNA can be extracted directly from the total tissue samplewithout further purification. Alternatively, if the density of cells,such as cancer cells, e.g., melanoma cells, in a tissue sample is low(less than about 1%), additional procedures to enrich the tissue samplefor melanoma cells can be performed. DNA also can be isolated fromfresh/frozen tissue, a fine-needle aspirate, or peripheral blood.

The sample may be prepared for assay using any suitable method as isknown in the art. Desirably, the method extracts and concentratesnucleic acids. The method also desirably makes the target sequenceaccessible for amplification, and removes potential inhibitors ofamplification from the extract.

DNA can be isolated from peripheral blood using, for example, a DNeasyDNA isolation kit, a QIAamp DNA blood kit, or a PAXgene blood DNA kitfrom Qiagen Inc. (Valencia, Calif.), or other methods known to one ofordinary skill in the art. DNA from other tissue samples also can beobtained using a DNeasy DNA isolation kit. Any other DNA extraction andpurification technique also can be used, including liquid-liquid andsolid-phase techniques ranging from phenol-chloroform extraction toautomated magnetic bead nucleic acid capture systems. RNA can beisolated and reverse-transcribed and the resulting cDNA can be amplified(e.g., reverse-transcription polymerase chain reaction (RT-PCR) asdescribed in U.S. Pat. Nos. 5,310,652; 5,322,770; 5,561,058; 5,641,864;and 5,693,517, for example).

Once nucleic acid has been obtained, it can be contacted with primersthat result in specific amplification of a mutant sequence, if themutant sequence is present in the sample. “Specific amplification” meansthat the primers amplify a specific mutant sequence and not other mutantsequences or the wild-type sequence. See, e.g., PCR Technology:Principles and Applications for DNA Amplification (Erlich, Editor,Freeman Press, NY (1992)); PCR Protocols: A Guide to Methods andApplications (Innis, et al., Editors, Academic Press, San Diego, Calif.(1990)); Current Protocols in Molecular Biology (Ausubel, 1994-1999,including supplemental updates through April 2004); and MolecularCloning: A Laboratory Manual (Sambrook & Russell, 3rd ed., 2001).Allele-specific amplification-based methods or extension-based methodsare described in Int'l Pat. App. Pub. No. WO 93/22456 and U.S. Pat. Nos.4,851,331; 5,137,806; 5,595,890; and 5,639,611, all of which arespecifically incorporated herein by reference for their teachingsregarding same. While methods such as ligase chain reaction, stranddisplacement assay, and various transcription-based amplificationmethods can be used (see, e.g., review by Abramson and Myers, CurrentOpinion in Biotechnology 4:41-47 (1993)), PCR, in particular PCRemploying clamps, such as PNA clamps, is preferred.

Multiple allele-specific primers, such as multiple mutant alleles orvarious combinations of wild-type and mutant alleles, can be employedsimultaneously in a single amplification reaction. Amplificationproducts can be distinguished by different labels or size (e.g., usinggel electrophoresis).

A primer can be detectably labeled with a label that can be detected byspectroscopic, photochemical, biochemical, immunochemical or chemicalmeans, for example (see, e.g., Sambrook, et al.). Useful labels includea dye, such as a fluorescent dye, a radioactive label, such as ³²P, anelectron-dense reagent, an enzyme, such as peroxidase or alkalinephosphatase, biotin, or haptens and proteins for which antisera ormonoclonal antibodies are available.

A detectable oligonucleotide can be similarly labeled, such as withfluorescein. In this regard, if the primer is labeled with a dye and thedetectable oligonucleotide is labeled with fluorescein and is designedto bind to the nascent strand opposite from the dye, fluorescenceresonance energy transfer (FRET) across the DNA helix can occur.

Other detectable oligonucleotides include a molecular probe, a TAQMAN®probe, a single-stranded DNA probe, a double-stranded DNA probe, and thelike.

Any suitable sequence can be used as the IC. Examples of IC targetsequences include those used in the EXAMPLES herein.

Nucleic acid amplification reagents include an enzyme having polymeraseactivity (e.g., AmpliTaq Gold®), one or more enzyme co-factors (e.g.,MgCl₂), and deoxynucleotide triphosphates (dNTPs; e.g., dATP, dGTP,dCTP, and dTTP).

Conditions that promote amplification are those that promote annealingof primers and extension of nucleic acid sequences. Annealing isdependent on various parameters, such as temperature, ionic strength,length of sequences being amplified, complementarity, and G:C content ofthe sequences being amplified. For example, lowering the temperaturepromotes annealing of complementary nucleic acid sequences. High G:Ccontent and longer length stabilize duplex formation. Generally, primersand detectable oligonucleotides of about 30 bp or less and having a highG:C content work well. Preferred amplification conditions, primers anddetectable oligonucleotides are exemplified herein.

Amplification can be repeated any suitable number of times by thermalcycling the reaction mixture between about 10 and about 100 times, suchas between about 20 and about 75 times, such as between about 25 andabout 50 times.

Once the amplification reactions are completed, the presence of anamplified product can be detected using any suitable method. Suchmethods include, without limitation, those known in the art, such as gelelectrophoresis with or without a fluorescent dye (depending on whetherthe product was amplified with a dye-labeled primer), a melting profilewith an intercalating dye (see, e.g., PCR Technology, Principles, andApplications for DNA Amplification, Erlich, Ed., W. H. Freeman and Co.,New York, 1992, Chapter 7), and hybridization with an internaldetectable oligonucleotide. Other examples of methods includeenzyme-linked immunosorbent assay (ELISA), electro-chemiluminescence,reverse dot blots, high pressure liquid chromatography (HPLC) (see,e.g., Lazar, Genome Res. 4: S1-S14 (1994)), and single-strandconformation polymorphism analysis of single-stranded PCR products alsocan be used (see, e.g., Orita, et al., PNAS USA 86: 2766-2770 (1989)).

Amplified nucleic acid can be detected by monitoring an increase in thetotal amount of double-stranded DNA (dsDNA) in the reaction mixture(see, e.g., U.S. Pat. No. 5,994,056 and European Pat. Pub. Nos. 487,218and 512,334). A DNA-binding dye, such as SYBR Green, is used. The dyefluoresces when bound to dsDNA, and the increase in fluorescence is usedto determine the increase in dsDNA.

Dideoxy sequencing-based methods and Pyrosequencing™ ofoligonucleotide-length products also can be used to detect amplifiednucleic acid. Another sequencing method is described by Kobayashi, etal., Mol. Cell. Detectable oligonucleotides 9: 175-182 (1995)).

When PCR is issued, conditions, such as those exemplified in theEXAMPLES herein, can be used. When standard PCR is used, detection canoccur after amplification is complete, such as after using a labeledprimer during amplification, by using a labeled primer as a detectableoligonucleotide after amplification, or by using a detectableoligonucleotide, which differs in sequence from the primers, afteramplification to hybridize to the amplified target sequence. Labeledamplification products then can be separated and detected by othermeans.

Alternatively, the amplification and detection can be combined in areal-time PCR assay. When real-time PCR is used, the mixture can furthercomprise nucleic acid detection reagents, such as a non-specificfluorescent dye that intercalates with any double-stranded DNA, forexample, or a sequence-specific DNA detectable oligonucleotide, whichpermits detection only after the detectable oligonucleotide hybridizeswith its complementary DNA target, thereby enabling simultaneousamplification and detection. When a detectable oligonucleotide ispresent in the mixture during amplification, the detectableoligonucleotide should be stable under the conditions that promoteamplification, should not interfere with amplification, should bind toits target sequence under amplification conditions, and emit a signalonly upon binding its target sequence. Examples of detectableoligonucleotide that are particularly well-suited in this regard includemolecular beacon detectable oligonucleotides, TAQMAN® detectableoligonucleotides, and linear detectable oligonucleotides, such as thosedescribed by Abravaya, et al. (U.S. Pat. App. Pub. No. 2005/0227257).The detectable oligonucleotides can form the loop region, alone or infurther combination with part of the stem region, of a molecular beacon.The detectable oligonucleotides also can be used as linear detectableoligonucleotides with a fluorophore (e.g., FAM) at one end and ahigh-efficiency quencher, such as the Black Hole Quencher (BHQ®;BioSearch Technologies, Inc., Novato, Calif.), at the other end.

The detection of an amplified product indicates, for example, that cellscontaining a specific mutant BRAF gene or genes (depending on whether ornot two or more mutant BRAF genes are simultaneously detected) werepresent in the sample, while the lack of detection of an amplifiedproduct indicates that cells containing a specific mutant BRAF gene werenot present in the sample, such as when cancer is present but has notmetastasized. In this regard, if two or more specific mutant BRAF genesare amplified at the same time (or one or more specific mutant BRAFgenes and wild-type BRAF), a primer for each specific mutant BRAF can belabeled with a distinct detectable label, thereby enabling the detectionof two or more specific mutant BRAFs (or one or more specific mutantBRAFs and wild-type BRAF gene) to be distinguished. The relative levelsof mutant and wild-type products can indicate the fraction of cells inthe sample that contain a specific mutant BRAF gene. Lower fractions ofcells containing the mutant BRAF sequence can indicate lower levels ofmetastasis, while higher fractions of cells containing the mutantsequence can indicate higher levels of metastasis.

If desired, the method can further comprise an initial universalamplification step. For example, the sample can be contacted withdegenerate primers and amplified prior to specific amplification of oneor more mutant BRAF genes, alone or in further combination withwild-type BRAF or an internal control sequence.

Preferably, the method employs a PNA clamp (see, e.g., Demers, et al.,Nucleic Acids Res. 23: 3060-3065 (1995)). The PNA clamp preferablyinhibits or prevents amplification of wild-type BRAF or whichever mutantBRAF gene is most prevalent in relation to the specific mutant BRAF geneto be amplified.

If desired, the nucleic acid sample or the detectable oligonucleotidecan be immobilized on a solid support. Examples of assay formatsutilizing solid supports include dot-blot formats and reverse dot-blotformats (see, e.g., U.S. Pat. Nos. 5,310,893; 5,451,512; 5,468,613; and5,604,099, all of which are specifically incorporated herein byreference for their teachings regarding same).

Following amplification, it may be desirable to separate theamplification product from the template and the excess primer todetermine whether specific amplification occurred. Separation can beeffected by agarose, agarose-acrylamide or polyacrylamide gelelectrophoresis using standard methodology (see, e.g., Sambrook, et al.,Molecular Cloning, Fritsch and Maniatis, eds., Cold Spring Harbor Lab.Press, Cold Spring Harbor, N.Y. (1989)). Alternatively, chromatographycan be used to effect separation. Examples of type of chromatographyinclude adsorption, partition, ion-exchange and molecular sieve, andexamples of types of chromatographic techniques include column, paper,thin-layer and gas chromatography (see, e.g., Freifelder, PhysicalBiochemistry Applications to Biochemistry and Molecular Biology, 2nded., Wm. Freeman & Co., New York, N.Y. (1982)).

Amplification is confirmed by visualization. For example, a gel stainedwith ethidium bromide can be visualized with UV light. Amplificationproducts labeled with a radioisotope can be visualized by exposing anddeveloping an x-ray film, whereas amplification products labeled with afluorometric label can be visualized by subjecting the amplificationproducts to stimulating spectra. A preferred method of visualization ofamplification is the use of a labeled detectable oligonucleotide thathybridizes to the amplified products. A manual column, such as oneavailable from Qiagen, also can be used.

The use of an automated sample preparation system, such as an automatedsample preparation system designed to use magnetic microparticleprocesses for the purification of nucleic acids, can be preferred. Anexample of an automated sample preparation system is m2000sp, which isavailable from Abbott Laboratories, Abbott Park, Ill. Alternatively,samples can be prepared using the m24sp automated sample preparationsystem (Abbott) or prepared manually. Automated sample preparation ispreferred over manual preparation because it is more consistent. Anotherexample of a sample preparation kit is the QIAamp DNA FFPE tissue kit,which is available from Qiagen.

The Abbott mSample Preparation System_(DNA) (4×24 preps; Abbott)reagents capture the nucleic acids and remove unbound sample components.Proteinase K is included in the lysis step to digest proteins associatedwith the samples. The bound nucleic acids are eluted and transferred toa 96-well deep plate. The nucleic acids are then ready foramplification. An unrelated DNA sequence, which serves as an internalcontrol (IC) to demonstrate that the process has proceeded correctly foreach sample, is introduced into the sample preparation procedure and isprocessed along with the calibrators, controls, and specimens.

Amplification/detection can be carried out as known in the art, such asby use of the m2000rt instrument (Abbott Molecular Inc., Des Plaines,Ill.). The target nucleic acid (e.g., DNA, RNA or both) is amplified byDNA polymerase reverse transcriptase in the presence of deoxynucleotidetriphosphates (dNTPs) and an activation agent, for example, magnesium ormanganese. The amplification reagent contains specific sets ofamplification primers for the specific mutant (e.g., mutant BRAF) and,preferably, an IC. During PCR amplification, high temperature is used toseparate the strands of double-stranded DNA. When the reaction is cooledto a temperature where DNA annealing can occur, the analyte-specific,single-stranded DNA oligonucleotide primers bind to the analyte DNA. Theprimers are extended by DNA polymerase, thereby making an exact copy ofa short target stretch of the analyte DNA. The DNA polymerase can be,but need not be, a thermophilic enzyme that has been modified in itsactive site by a molecule that renders it inactive. When the enzyme isheated prior to the initiation of PCR, the inhibitory molecule iscleaved from the enzyme, thereby allowing it to regain its activity. Inthis manner, the enzyme is only active at temperatures where specificDNA-DNA interactions occur. This greatly reduces non-specific PCRartifacts, such as primer dimers. During each round of thermal cycling,amplification products dissociate to single strands at high temperature,allowing primer annealing and extension as the temperature is lowered.Exponential amplification of the target is achieved through repeatedcycling between high and low temperatures. Amplification of the specificmutant (e.g., mutant BRAF) and, if present, the IC targets takes placesimultaneously in the same reaction.

The method can be used to, for example, determine the BRAF mutationstatus for the purpose of evaluating treatment options with BRAFinhibitors, anti-EGFR monoclonal antibodies, MEK inhibitors, and thelike. For example, Zelboraf™ (vemurafenib; Roche) reportedly has beenshown to improve survival in people with BRAF V600E mutation-positivemetastatic melanoma.

The method also can be used to predict outcome for a patient diagnosedwith cancer, such as melanoma, to assess risk of metastasis, such as inpatients with early stages of disease (stage I/II), such as melanoma,and to monitor patients with advanced, metastatic cancer, such asmetastatic melanoma (stage III/IV). Since metastatic spread of canceroften occurs hematogenously, the method also can be used to assayperipheral blood to assess recurrence. Other cancers include, but arenot limited to, thyroid (e.g., papillary thyroid carcinomas (PTC),ovary, colorectal, stomach, pancreas, Barrett's adenocarcinoma, pleuralmesothelioma, non-Hodgkin's lymphoma, acute leukemia, squamous cellcarcinoma of the head and neck, prostate, breast, ovary (e.g., low-gradeserous carcinoma), hepatocellular carcinoma, sarcoma, pituitary, largeintestine, biliary tract, eye, central nervous system, hematopoietictissue, lymphoid tissue, rhabdomyosarcoma, sarcoma, glioma,cholangiocarcinoma, and lung adenocarcinoma.

In view of the above, a method of detecting at least one mutation (X) ofa codon in a gene in a sample of DNA is also provided. The methodcomprises:

(a) performing an amplification reaction with the sample of DNA, whereinthe amplification reaction comprises a primer, the last threenucleotides at the 3′ terminus of which encodes X and wherein the fourthnucleotide from the 3′ terminus contains a base other than adenine (A),wherein, if X is present, the primer anneals to X,

whereupon, if X is present, the amplification reaction produces anamplification product comprising X,

(b) detecting the amplification product comprising X, and

wherein, if X is encoded by more than one codon, the amplificationreaction comprises a primer for each codon. The amplification reactioncan further comprise (iii) at least one peptide nucleic acid (PNA)clamp, wherein at least one PNA clamp blocks the amplification fromwild-type target, and wherein, if the amplification reaction comprisesone or more other PNA clamps, the PNA preferably clamps a detectableoligonucleotide and/or a primer. Detecting the amplification productcomprising X can comprise detecting a labeled primer or contacting theamplification product with a detectable oligonucleotide and detectinghybridization of the detectable oligonucleotide to the amplificationproduct comprising X. The amplification reaction can further comprise aninternal control primer, in which case the amplification reaction alsoproduces an amplification product comprising the internal control, inwhich case step (b) includes detecting the amplification productcomprising the internal control. Detecting the amplification productcomprising the internal control can comprise detecting a labeled primeror contacting the amplification product with a detectableoligonucleotide and detecting hybridization of the detectableoligonucleotide to the amplification product comprising the internalcontrol. When the method comprises detecting two or more X, the methodcan comprise performing an amplification reaction with the sample of DNAfor each X together or separately. In this regard, the method also canfurther comprise determining which X is present in the sample of DNA.

Primers, Detectable Oligonucleotides, and Method of Designing a Primer

A set of primers for amplification of V600X in exon 15 of the BRAF genein a sample of nucleic acid from a human is also provided. The set ofprimers comprises primers, such as forward primers, each of which is anoligonucleotide, which is about 15 to about 35 nucleotides in length andcomprises a nucleotide sequence encoding X at its 3′ terminus. The setof primers comprising primers for amplification of V600E comprises oneprimer encoding GAA at its 3′ terminus and another primer encoding GAGat its 3′ terminus. The set of primers for amplification of V600Kcomprises one primer encoding AAA at its 3′ terminus and another primerencoding AAG at its 3′ terminus. The set of primers comprising primersfor amplification of V600D comprises one primer encoding GAT at its 3′terminus and another primer encoding GAC at its 3′ terminus. The set ofprimers for amplification of V600N comprises one primer encoding AAT atits 3′ terminus and another primer comprising AAC at its 3′ terminus.The set of primers comprising primers for amplification of V600Rcomprises a primer encoding CGT at its 3′ terminus, a primer encodingCGC at its 3′ terminus, a primer encoding CGA at its 3′ terminus, aprimer encoding CGG at its 3′ terminus, a primer encoding AGA at its 3′terminus, and a primer encoding AGG at its 3′ terminus. With regard toall of the aforementioned primers, the remainder of the nucleotidesequence (i.e., the nucleotide sequence up to the 3′ terminal codon)should be such that a stable duplex will preferentially form between theprimer and the exactly complementary allelic sequence encoding V600X. Inother words, primers for amplification of V600E will preferentiallyamplify V600E but not others, such as V600, V600K, V600D, V600N, andV600R. Primers for amplification of V600K will preferentially amplifyV600K but not V600E, V600D, V600N, and V600R. Primers for amplificationof V600D will preferentially amplify V600D but not V600E, V600K, V600N,and V600R. Primers for amplification of V600N will preferentiallyamplify V600N but not V600E, V600K, V600D, and V600R. Preferably, aprimer for amplification of V600E in which E is encoded by GAA willpreferentially not amplify V600E in which E is encoded by GAG and viceversa, a primer for amplification of V600K in which K is encoded by AAAwill preferentially not amplify V600K in which K is encoded by AAG andvice versa, a primer for amplification of V600D in which D is encoded byGAT will preferentially not amplify V600D in which D is encoded by GACand vice versa, and a primer for amplification of V600N in which N isencoded by AAT will preferentially not amplify V600N in which N isencoded by AAC and vice versa. Likewise, a primer for amplification ofV600R in which R is encoded by CGT will preferentially not amplify V600Rin which R is encoded by CGC, CGA, CGG, AGA, and AGG, a primer foramplification of V600R in which R is encoded by CGC will preferentiallynot amplify V600R in which R is encoded by CGT, CGA, CGG, AGA, and AGG,a primer for amplification of V600R in which R is encoded by CGA willpreferentially not amplify V600R in which R is encoded by CGT, CGC, CGG,AGA, and AGG, a primer for amplification of V600R in which R is encodedby CGG will preferentially not amplify V600R in which R is encoded byCGT, CGC, CGA, AGA, and AGG, a primer for amplification of V600R inwhich R is encoded by AGA will preferentially not amplify V600R in whichR is encoded by CGT, CGC, CGA, CGG, and AGG, and a primer foramplification of V600R in which R is encoded by AGG will preferentiallynot amplify V600R in which R is encoded by CGT, CGC, CGA, CGG, and AGA.Preferably, the set of primers comprises at least one primer selectedfrom the group consisting of:

(a) an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACNGAA [SEQ ID NO: 44] at its 3′ terminus and/or anoligonucleotide comprising the nucleotide sequence GGTCTAGCTACNGAG [SEQID NO: 45] at its 3′ terminus,

(b) an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACNAAA [SEQ ID NO: 46] at its 3′ terminus and/or anoligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAG [SEQID NO: 47] at its 3′ terminus,

(c) an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACNGAT [SEQ ID NO: 48] at its 3′ terminus and/or anoligonucleotide comprising the nucleotide sequence GGTCTAGCTACNGAC [SEQID NO: 49] at its 3′ terminus,

(d) an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACNAAT [SEQ ID NO: 50] at its 3′ terminus and/or anoligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAC [SEQID NO: 51] at its 3′ terminus,

(e) an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACNCGT [SEQ ID NO: 52] at its 3′ terminus, an oligonucleotidecomprising the nucleotide sequence GGTCTAGCTACNCGC [SEQ ID NO: 53] atits 3′ terminus, an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACNCGA [SEQ ID NO: 54] at its 3′ terminus, an oligonucleotidecomprising the nucleotide sequence GGTCTAGCTACNCGG [SEQ ID NO: 55] atits 3′ terminus, an oligonucleotide comprising the nucleotide sequenceGGTCTAGCTACN AGA [SEQ ID NO: 56] at its 3′ terminus, and anoligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAGG [SEQID NO: 57] at its 3′ terminus,

(d) and (e),

(a) and (b),

(a) and (c),

(b) and (c),

(a), (b), and (c),

any of (a), (b), and (c), in further combination with (d),

any of (a), (b), and (c), in further combination with (e), and

any of (a), (b), and (c), in further combination with (d) and (e),

wherein N is a nucleotide containing a base other than adenine (A), and

wherein the oligonucleotide comprises from about 15 nucleotides to about35 nucleotides. By “any of (a), (b), and (c)” is meant (a), (b), (c),(a) and (b), (a) and (c), (b) and (c), and (a), (b), and (c). Theoligonucleotide can further comprise contiguous with the G at the 5′ endof the nucleotide sequence one or more contiguous nucleotides of thenucleotide sequence 5′ AATAGGTGATTTT 3′ [SEQ ID NO: 58] starting withthe T at the 3′ end of the nucleotide sequence. The set of primers canfurther comprise a primer, such as a reverse primer, comprising fromabout 15 nucleotides to about 35 nucleotides, wherein, when the primercomprises 15-27 nucleotides, it comprises 15-27 contiguous nucleotidesof SEQ ID NO: 10. The detectable oligonucleotide can comprise from about15 nucleotides to about 35 nucleotides, wherein, when the detectableoligonucleotide comprises 15-20 nucleotides, it comprises 15-20contiguous nucleotides of SEQ ID NO: 11.

Oligonucleotides can be prepared by any suitable method, usuallychemical synthesis (e.g., solid-phase synthesis) employing commerciallyavailable reagents and instruments (see, e.g., Applied Biosystems, Inc.(Foster City, Calif.), DuPont (Wilmington, Del.), and Milligen (Bedford,Mass.)). Alternatively, they can be purchased through commercialsources. Methods of synthesizing oligonucleotides are well-known in theart (see, e.g., Narang, et al., Meth. Enzymol. 68: 90-99 (1979); Brown,et al., Meth. Enzymol. 68: 109-151 (1979); Beaucag, et al., TetrahedronLett. 22: 1859-1862 (1981); and U.S. Pat. No. 4,458,066).

Multiple allele-specific primers, based on the genetic codon for theidentification of each mutated amino acid, are used. One primer isdesigned for each corresponding genetic codon encoding the mutation ofinterest at the 3′ end plus an intended mutation at the fourthnucleotide from the 3′ end. Allele-specific forward primers amplifyvariant specific targets based on select PCR amplification by a DNApolymerase, such as Taq polymerase, according to 3′ matches betweenprimers and template. A reverse transcriptase-DNA polymerase, such asrTth, also can be used in the context of the present methods. In thisregard, a mixture of RNA polymerases, DNA polymerases, or RNA and DNApolymerases can be used. The reverse primer and detectableoligonucleotide are based on consensus sequences shared betweenreactions.

Thus, in view of the above, also provided is a method of designing aprimer for detection of at least one mutation (X) of a codon in a genein a sample of nucleic acid. The method comprises synthesizing a primer,the last three nucleotides at the 3′ terminus of which encodes X andwherein the fourth nucleotide from the 3′ terminus contains a base otherthan that which is present in the wild-type gene, whereupon a primer fordetection of at least one mutation (X) in a codon in a gene in a sampleof nucleic acid is designed. The method of designing primers based onthe teachings of the present specification also include designingprimers for the detection of more than one SNP and for detecting geneswith target SNPs that also contain other, non-target mutants. Strategiesfor such primer design are given in Table 1.

Peptide nucleic acids (PNAs) are used as PCR clamping reagents that bindto complementary nucleic acid sequences with greater specificity andstability than their DNA counterparts (see, e.g., U.S. Pat. App. Pub.No. 2010/0009355 for discussion of PNA-based PCR clamping). The PNAsoverlap with the forward primers and match perfectly the non-specificsequences to be blocked. As a result, the PNAs bind to the non-specifictargets and inhibit the binding of primers to the same targets, therebysuppressing non-specific amplification (see FIG. 1).

Primers corresponding to a given amino acid position can be mixed foruse in an assay to detect all possible variants of a specific mutationat that position. For example, allele-specific primers carrying GAG andGAA at their 3′ end, respectively, can detect all possible variants forglutamic acid at amino acid position 600, such that all V600E mutationsare detected (see, FIGS. 1 and 2).

The ability to carry out the method in a closed-tube, homogeneous formatminimizes the risk of contamination (see, e.g., Kreuzer, et al., Ann.Hematol. 82: 284-289 (2003)). The sample can be contacted with a pair ofprimers by any means routinely applied for contacting a sample with apair of PCR primers. For example, the sample and the primers can becontacted in a microwell plate or in a microvial adapted for the mixtureof small volumes.

In view of the foregoing, provided are primers, such as forward primers,that amplify all possible V600E mutations in exon 15 of the human BRAFgene in a mutation-specific manner, primers, such as forward primers,that amplify all possible V600K mutations in exon 15 of the human BRAFgene in a mutation-specific manner, primers, such as forward primers,that amplify all possible V600D mutations in a mutation-specific manner,primers, such as forward primers, that amplify all possible V600Rmutations in a mutation-specific manner, primers, such as forwardprimers, that amplify all possible V600N mutations in amutation-specific manner, detectable oligonucleotides and PNAs to blockthe non-specific amplification of non-targeted BRAF sequences so as toincrease specificity and sensitivity, and primers and detectableoligonucleotides to detect BRAF genomic sequences close to exon 15 toserve as internal controls (e.g., DNA adequacy, sample extraction,amplification efficiency, and standardization of the relativequantification of mutations (e.g., as a percentage of total wild-typeand mutant alleles)). Also provided are diagnostic real-time PCR (rtPCR)methods that use the aforementioned primers and detectableoligonucleotides to amplify and detect V600 mutations in exon 15 of thehuman BRAF gene in separate reactions or a pooled reaction.

Primers that are at least about 80% identical with the primers describedherein also can be used. If desired, one or both primers (i.e., forwardand reverse primers) can be tagged or labeled. Use of labeled primersresults in labeled amplification products. Fluorescently labeledamplification products can be detected using any suitable equipmentdesigned to detect fluorescence, such as the ABI 3100 Genetic Analyzerand Genescan 3.1.2 software (Applied Biosystems), for example.

While the methods described herein are based on the detection ofgenomic, DNA, RNA-based assays can be used. However, such assays arebased on reverse transcription and subsequent amplification of mRNA fromwhole blood. While the sensitivity of mRNA-based methods generally isgood, RNA degradation and low efficiency of the reverse transcriptasecan limit, even severely limit, the practicality of such assays. Inaddition, because the amount of mRNA of interest can vary widely, forexample, depending on the metabolic state of the circulating cells, theresults of the assays can be difficult to reproduce.

If desired, the primers described above can be modified so that they nolonger act as primers for DNA synthesis and can be labeled and used asdetectable oligonucleotides. The detectable oligonucleotides can be usedin different assay formats to detect a mutation (X) of the codonencoding valine at amino acid position 600 (V600X) in exon 15 of theBRAF gene in a sample of nucleic acid, such as DNA. For example, thedetectable oligonucleotides can be used in a 5′-nuclease assay (see,e.g., U.S. Pat. Nos. 5,210,015; 5,487,972; and 5,804,375; and Holland,et al., PNAS USA 88: 7276-7280 (1988), all of which are specificallyincorporated by reference for their teachings regarding same).

While the primers and detectable oligonucleotides have been describedherein in the context of their use in nucleic acid-based amplificationmethods, such as PCR, in particular real-time PCR, such primers anddetectable oligonucleotides can be useful as detectable oligonucleotidesin other nucleic acid-based methods, such as hybridization techniques(e.g., membrane-based hybridization techniques (Southern blots andNorthern blots), modified nucleic acid hybridization techniques (see,e.g., Pandian, et al., U.S. Pat. No. 5,627,030), and enzyme-linkedimmunoadsorbent assay (ELISA)-like techniques), which are used to detectidentical, similar and complementary polynucleotide sequences.

The detectable oligonucleotides, which are single-stranded, linear DNAoligonucleotides, are detectably labeled in accordance with methodsknown in the art. Alternatively, primers can be similarly labeled, ifdesired. Any suitable label, such as a fluorophore, a luminophore, achemiluminophore, a photoluminophore, or a radioisotope, can be used.For example, a fluorescent moiety can be covalently linked to one end ofthe detectable oligonucleotide and a quenching moiety can be covalentlylinked to the other end. Examples of suitable fluorophores include, butare not limited to, FAM (e.g., 6′-FAM), fluorescein and derivativesthereof, rhodamine, coumarin and derivatives thereof, TET, HEX, JOE,TAMA, TAMRA, NTB, ROX, VIC, NED, 4,7-dichloro-fluorescein,4,7-dichloro-rhodamine, DABCYL, DABSYL, malachite green, LC-Red 610,LC-Red 640, LC-Red 670, LC-Red 705, Lucifer yellow, TEXAS RED®,tetramethylrhodamine, tetrachloro-6-carboxyfluoroscein,5-carboxyrhodamine, and cyanine dyes (e.g., Cy3 and Cy5) and derivativesthereof. FAM is a preferred label. Examples of quenchers include DABCYL,DABSYL, DABMI, tetramethylrhodamine, TAMRA, and BHQ® dyes. As indicatedabove, during each round of real-time PCR amplification, the detectablylabeled detectable oligonucleotides anneal to the amplified target DNA,if present. In the absence of a target sequence, each of the detectableoligonucleotides adopts a conformation that brings the quencher closeenough to the excited fluorophore to absorb its energy before it can befluorescently emitted. In the presence of a target sequence, eachdetectable oligonucleotide binds to its complementary sequence in thetarget and the fluorophore and the quencher are held apart, allowingfluorescent emission and detection. Preferably, the target-specificdetectable oligonucleotides and the IC-specific detectableoligonucleotides are labeled differently so that target DNA and IC DNAcan be distinguished. In this regard, the target-specific detectableoligonucleotide(s) is/are preferably labeled with FAM and quenched withBHQ-1.

Kit

A kit is also provided. The kit comprises:

(i) a set of primers for detection of V600X in exon 15 of the BRAF genein a sample of nucleic acid from a human, wherein the set of primerscomprises at least one primer selected from the group consisting of:

-   -   (a) an oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNGAA [SEQ ID NO: 44] at its 3′ terminus and/or an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNGAG [SEQ ID NO: 45] at its 3′ terminus,    -   (b) an oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNAAA [SEQ ID NO: 46] at its 3′ terminus and/or an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNAAG [SEQ ID NO: 47] at its 3′ terminus,    -   (c) an oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNGAT [SEQ ID NO: 48] at its 3′ terminus and/or an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNGAC [SEQ ID NO: 49] at its 3′ terminus,    -   (d) an oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNAAT [SEQ ID NO: 50] at its 3′ terminus and/or an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNAAC [SEQ ID NO: 51] at its 3′ terminus,    -   (e) an oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNCGT [SEQ ID NO: 52] at its 3′ terminus, an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNCGC [SEQ ID NO: 53] at its 3′ terminus, an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNCGA [SEQ ID NO: 54] at its 3′ terminus, an        oligonucleotide comprising the nucleotide sequence        GGTCTAGCTACNCGG [SEQ ID NO: 55] at its 3′ terminus, an        oligonucleotide comprising the nucleotide sequence GGTCTAGCTACN        AGA [SEQ ID NO: 56] at its 3′ terminus, and an oligonucleotide        comprising the nucleotide sequence GGTCTAGCTACNAGG [SEQ ID NO:        57] at its 3′ terminus,    -   (d) and (e),    -   (a) and (b),    -   (a) and (c),    -   (b) and (c),    -   (a), (b), and (c),    -   any of (a), (b), and (c), in further combination with (d),    -   any of (a), (b), and (c), in further combination with (e), and    -   any of (a), (b), and (c), in further combination with (d) and        (e),

wherein N is a nucleotide containing a base other than adenine (A), and

wherein the oligonucleotide comprises from about 15 nucleotides to about35 nucleotides, and

(ii) instructions for a method of detecting a mutation (X) of the codonencoding valine at amino acid position 600 (V600X) in exon 15 of theBRAF gene in a sample of nucleic acid from a human, which methodcomprises:

(a) performing an amplification reaction with the sample of nucleicacid, wherein the amplification reaction comprises a primer, the lastthree nucleotides at the 3′ terminus of which encodes X and wherein thefourth nucleotide from the 3′ terminus contains a base other thanadenine (A), wherein, if X is present, the primer anneals to X, and atleast one peptide nucleic acid (PNA) clamp, wherein at least one PNAclamp blocks the amplification from wild-type target,

wherein, if the sample of nucleic acid is mRNA, step (a) furthercomprises obtaining cDNA reverse-transcribed from the mRNA orreverse-transcribing cDNA from the mRNA before performing theamplification reaction,

whereupon, if X is present, the amplification reaction produces anamplification product comprising X, and

(b) detecting the amplification product comprising X,

wherein, if X is encoded by more than one codon, the amplificationreaction comprises a primer for each codon,

wherein, if the method comprises detecting two or more X, the method cancomprise performing an amplification reaction with the sample of nucleicacid for each X together or separately, and

wherein the method also can further comprise determining which X ispresent in the sample of nucleic acid. The oligonucleotide can furthercomprise contiguous with the G at the 5′ end of the nucleotide sequenceone or more contiguous nucleotides of the nucleotide sequence 5′AATAGGTGATTTT 3′ [SEQ ID NO: 58] starting with the T at the 3′ end ofthe nucleotide sequence. The kit can further comprise a primer, such asa reverse primer, comprising from about 15 nucleotides to about 35nucleotides, wherein, when the primer comprises 15-27 nucleotides, itcomprises 15-27 contiguous nucleotides of SEQ ID NO: 10.

The kit can further comprise a detectable oligonucleotide comprisingfrom about 15 nucleotides to about 35 nucleotides, wherein, when thedetectable oligonucleotide comprises 15-20 nucleotides, it comprises15-20 contiguous nucleotides of SEQ ID NO: 11. X can be at least oneamino acid selected from the group consisting of E, K, D, R, and N. Xcan be at least one amino acid selected from the group consisting of E,K, and D, such as E, E and K, E and D, K and D, or E, K, and D. Anexample of a label is FAM. In this regard, the label FAM is preferablyused in combination with the quencher BHQ-1.

A kit can contain a container or a sample vial for storing a sample of atissue or a body fluid. The primers, such as a pair of primers,specifically a forward primer and a reverse primer, can be in acomposition in amounts effective to permit detection of mutantsequences. Detection of mutant sequences is accomplished using any ofthe methods described herein or known in the art for detecting aspecific nucleic acid molecule in a sample, A kit can also comprisebuffers, nucleotide bases, and other compositions to be used inhybridization and/or amplification reactions.

The kit can further comprise dNTPs. Preferably, the dNTPs are suppliedin a buffered solution with a reference dye.

The primers, detectable oligonucleotides and dNTPs can be packaged invarious configurations. Preferably, the primers, detectableoligonucleotides and dNTPS are in a single container. The containerpreferably also contains a preservative, such as sodium azide and/orProClin® 950.

The kit can further comprise a DNA polymerase, an RNA polymerase, areverse transcriptase, and a mixture of two or more of the foregoing.Any suitable DNA polymerase can be used. An example of a preferred DNApolymerase is AmpliTaq Gold® (Life Technologies Corp., Carlsbad,Calif.). Likewise, any suitable RNA polymerase can be used. An exampleof a preferred reverse transcriptase-DNA polymerase is rTth. Thepolymerase can be supplied in a buffered solution, which optionallycontains, and preferably does contain, stabilizers.

The kit can further comprise an activation reagent, such as magnesiumchloride, in a buffered solution. The buffered solution preferablyincludes a preservative, such as sodium azide and/or ProClin® 950.

The kit can optionally further comprise an IC. The IC is an unrelatedDNA sequence that demonstrates that the process has proceeded correctlyfor each sample. Any suitable sequence can be used as the IC. Examplesof IC target sequences include those set forth in the EXAMPLES herein.The target-specific detectable oligonucleotides and the IC-specificdetectable oligonucleotides are labeled differently so that target DNAand IC DNA can be distinguished. An example of a label for theIC-specific detectable oligonucleotide is Cy5. Preferably, the label Cy5is used in combination with the quencher BHQ-2.

All patents, patent application publications, journal articles,textbooks, and other publications mentioned in the specification areindicative of the level of skill of those in the art to which thedisclosure pertains. All such publications are incorporated herein byreference to the same extent as if each individual publication werespecifically and individually indicated to be incorporated by reference.

The invention illustratively described herein may be suitably practicedin the absence of any element(s) or limitation(s), which is/are notspecifically disclosed herein. Thus, for example, each instance hereinof any of the terms “comprising,” “consisting essentially of,” and“consisting of” may be replaced with either of the other two terms.Likewise, the singular forms “a,” “an,” and “the” include pluralreferences unless the context clearly dictates otherwise. Thus, forexample, references to “the method” includes one or more methods and/orsteps of the type, which are described herein and/or which will becomeapparent to those ordinarily skilled in the art upon reading thedisclosure.

The terms and expressions, which have been employed, are used as termsof description and not of limitation. In this regard, where certainterms are defined under “Definitions” and are otherwise defined,described, or discussed elsewhere in the “Detailed Description,” allsuch definitions, descriptions, and discussions are intended to beattributed to such terms. There also is no intention in the use of suchterms and expressions of excluding any equivalents of the features shownand described or portions thereof. Furthermore, while subheadings, e.g.,“Definitions,” are used in the “Detailed Description,” such use issolely for ease of reference and is not intended to limit any disclosuremade in one section to that section only; rather, any disclosure madeunder one subheading is intended to constitute a disclosure under eachand every other subheading.

It is recognized that various modifications are possible within thescope of the claimed invention. Thus, it should be understood that,although the present invention has been specifically disclosed in thecontext of preferred embodiments and optional features, those skilled inthe art may resort to modifications and variations of the conceptsdisclosed herein. Such modifications and variations are considered to bewithin the scope of the invention as defined by the appended claims.

EXAMPLES

The following examples serve to illustrate the present disclosure. Theexamples are not intended to limit the scope of the claimed invention inany way.

Example 1

This example describes reactions for detection of individual SNPs atV600 in exon 15 of the BRAF gene in DNA.

Two alleles (i.e., codons) are possible for V600E, V600K, and V600Dmutation (i.e., GAG and GAA for glutamic acid (E), AAG and AAA forlysine (K), and GAT and GAC for aspartic acid (D)). Each forward primerwas designed to amplify preferentially a specific codon. Thus, twoforward primers are included in each reaction to ensure the completedetection of each amino acid mutation.

BRAF reverse primer and, when used, detectable oligonucleotide targetconsensus sequences. Therefore, the reverse primer and, when used, thedetectable oligonucleotide can be the same for all reactions.

Internal control primers and detectable oligonucleotide target asequence within exon 13 of the BRAF gene. They were the same for allreactions.

PNAs, which are very short, non-extendable oligonucleotides, areincluded to block potential non-specific amplification. They bind totheir complementary target sequences in a highly sequence-specificmanner. Since PNA sequences are on the same strand as the forwardprimer, they compete with the forward primer and prevent non-specificamplification. Even though there are multiple non-specific SNPs for anygiven mutation-specific PCR, only the most prevalent ones, which maygenerate non-specific amplification, need to be blocked by PNAs, such aswild-type and V600K in the case of V600E detection, wild-type and V600Ein the case of V600K detection, and wild-type in the case of V600Ddetection.

The method comprised forming a mixture containing the oligonucleotidesand other components essential for nucleic acid amplification (e.g.,dNTP mix, buffer, enzyme, and divalent ion as activation agent),combining the mixture with purified nucleic acids, and subjecting thereaction mixture to specific conditions to amplify and detect the targetsequences. The processes were carried out in a closed tube format by aninstrument capable of concurrent thermal cycling and signal detection.Genomic DNA extracted from cell lines, formalin-fixed paraffin-embedded(FFPE) cell lines, and clinical FFPE tumor samples was assayed. Thespecificity of the assay was evaluated using genomic DNA extracted fromcell lines that carry wild-type or various BRAF mutations. Thesensitivity was evaluated using a mixture of wild-type BRAF cells andV600E mutant BRAF cells at defined ratios.

TABLE 1 V600E Reaction Sequence and Label (5′→3′ for DNA Oligonucleotide and N→C for PNA) Concentration** BRAF V600E forwardAATAGGTGATTTTGGTCTAGCTACCGAG [SEQ ID  0.2 μM primer 1 NO: 8]BRAF V600E forward AATAGGTGATTTTGGTCTAGCTACCGAA [SEQ ID  0.2 μM primer 2NO: 9] BRAF reverse primer TAATCAGTGGAAAAATAGCCTCAATTC [SEQ ID  0.2 μMNO: 10] BRAF detectable FAM-LGGAGLGGGLFFFALFAGLL-BHQ1-dT* [SEQ  0.2 μMoligonucleotide ID NO: 11] BRAF wild-type PNAGCTACAGTGAAATCTCG [SEQ ID NO: 12]  1 μM BRAF V600K PNAGCTACAAAGAAATCTCG [SEQ ID NO: 13]  1 μM Internal ControlGTATCACCATCTCCATATCATTGAGACC [SEQ ID  0.2 μM exon 13 forward primerNO: 14] Internal Control ACAAGACATTTAACGAATGGAACTTACTC [SEQ ID  0.2 μMexon 13 reverse primer NO: 15] Internal Control exon 13Quasar-GFAFGAFAGAFLGFAFAGG-BHQ2-dT*  0.2 μM detectable oligonucleotide[SEQ ID NO: 16] PCR oligo buffer  0.632 X dNTPs  0.4 mM ROX  0.0147 μMTaqGold 11 Units MgCl₂  4 mM *F = 5-Propynyl dC, L = 5-Propynyl dU**Concentration in 50 μl reaction consisting of 25 μl target and 25 μlPCR reagents

TABLE 2 V600K Reaction Sequence and Label (5′→3′ for DNA Oligonucleotide and N→C for PNA) Concentration** BRAF V600K forwardAATAGGTGATTTTGGTCTAGCTACTAAG [SEQ ID NO:  0.2 μM primer 1 17]BRAF V600K forward AATAGGTGATTTTGGTCTAGCTACTAAA  0.2 μM primer 2[SEQ ID NO: 18] BRAF reverse primerTAATCAGTGGAAAAATAGCCTCAATTC [SEQ ID NO: 10]  0.2 μM BRAF detectableFAM-LGGAGLGGGLFFFALFAGLL-BHQ1-dT* [SEQ ID  0.2 μM oligonucleotideNO: 11] BRAF wild-type PNA GCTACAGTGAAATCTCG [SEQ ID NO: 12]  1 μMBRAF V600E PNA GCTACAGAGAAATCTCG [SEQ ID NO: 19]  1 μM Internal ControlGTATCACCATCTCCATATCATTGAGACC  0.2 μM exon 13 forward primer[SEQ ID NO: 14] Internal ControlACAAGACATTTAACGAATGGAACTTACTC [SEQ ID NO:  0.2 μM exon 13 reverse primer15] Internal Control exon 13 Quasar-GFAFGAFAGAFLGFAFAGG-BHQ2-dT* [SEQ ID 0.2 μM detectable oligonucleotide NO: 16] PCR oligo buffer  0.632 XdNTPs  0.4 mM ROX  0.0147 μM TaqGold 11 Units MgCl₂  4 mM *F =5-Propynyl dC, L = 5-Propynyl dU **Concentration in reaction of 25 μltarget and 25 μl PCR reagents

TABLE 3 V600D Reaction Sequence and Label (5′→3′ for DNA Oligonucleotide and N→C for PNA) Concentration** BRAF V600D forwardAATAGGTGATTTTGGTCTAGCTACTGAT [SEQ ID NO:  0.2 μM primer 1 20]BRAF V600D forward AATAGGTGATTTTGGTCTAGCTACTGAC [SEQ ID NO:  0.2 μMprimer 2 21] BRAF reverse primerTAATCAGTGGAAAAATAGCCTCAATTC [SEQ ID NO: 10]  0.2 μM BRAF detectableFAM-LGGAGLGGGLFFFALFAGLL-BHQ1-dT* [SEQ ID  0.2 μM oligonucleotideNO: 11] BRAF wild-type PNA GCTACAGTGAAATCTCG [SEQ ID NO: 12]  1 μMInternal Control GTATCACCATCTCCATATCATTGAGACC  0.2 μMexon 13 forward primer [SEQ ID NO: 14] Internal ControlACAAGACATTTAACGAATGGAACTTACTC [SEQ ID NO:  0.2 μM exon 13 reverse primer15] Internal Control Quasar-GFAFGAFAGAFLGFAFAGG-BHQ2-dT* [SEQ ID  0.2 μMexon 13 detectable NO: 16] oligonucleotide PCR oligo buffer  0.632 XdNTPs  0.4 mM ROX  0.0147 μM TaqGold 11 Units MgCl₂  4 mM *F =5-Propynyl dC, L = 5-Plopynyl dU **Concentration in reaction of 25 μltarget and 25 μl PCR reagents

PCR cycling included one cycle at 92° C. for 10 minutes (TaqGoldactivation) and 55 cycles (the number of cycles can be modified) of 88°C./5 seconds, 92° C./15 seconds, 67° C./5 seconds, and 63° C./35 seconds(DNA amplification and fluorescence readings). Alternatively, PCRcycling can include one cycle at 92° C. for 10 minutes (TaqGoldactivation) and 55 cycles of 92° C. for 15 seconds, and 65° C. for 35seconds (DNA amplification and fluorescence readings).

A linearity study on 10 ng genomic DNA using the V600E assay and theV600K assay revealed a good linear relationship. A linearity study on2.5 ng genomic DNA extracted from FFPE cell line samples using the V600Eassay also revealed a good linear relationship.

Other mutations can be detected in the same manner. Allele-specificprimers can be designed for other mutations in the same manner asdescribed above for V600E/K/D SNPs.

Example 2

This example describes a pooled reaction for detection of multiple SNPsat V600 in exon 15 of the BRAF gene.

Two or more of BRAF V600E, V600K, and V600D mutations also can bedetected in a pooled reaction.

TABLE 4 V600 E/K/D Pooled Reaction Sequence and Label (5′→3′ for DNA Oligonucleotide and N→C for PNA) Concentration** BRAF V600E forwardAATAGGTGATTTTGGTCTAGCTACCGAG [SEQ ID NO: 8]  0.2 μM primer 1BRAF V600E forward AATAGGTGATTTTGGTCTAGCTACCGAA [SEQ ID NO: 9]  0.2 μMprimer 2 BRAF V600K forward AATAGGTGATTTTGGTCTAGCTACTAAG [SEQ ID NO: 0.2 μM primer 1 17] BRAF V600K forwardAATAGGTGATTTTGGTCTAGCTACTAAA [SEQ ID NO:  0.2 μM primer 2 18]BRAF V600D forward AATAGGTGATTTTGGTCTAGCTACTGAT [SEQ ID NO:  0.2 μMprimer 1 20] BRAF V600D forward AATAGGTGATTITGETCTAGCTACTGAC [SEQ ID NO: 0.2 μM primer 2 21] BRAF reverse primerTAATCAGTGGAAAAATAGCCTCAATTC [SEQ ID NO: 10]  0.2 μM BRAF detectableFAM-LGGAGLGGGLFFFALFAGLL-BHQ1-dT* [SEQ ID  0.2 μM oligonucleotideNO: 11] BRAF wild-type PNA GCTACAGTGAAATCTCG [SEQ ID NO: 12]  0.2 μMInternal Control GTATCACCATCTCCATATCATTGAGACC [SEQ ID NO: 14]  0.2 μMexon 13 forward primer Internal ControlACAAGACATTTAACGAATGGAACTTACTC [SEQ ID NO:  0.2 μM exon 13 reverse primer15] Internal Control Quasar-GFAFGAFAGAFLGFAFAGG-BHQ2-dT* [SEQ ID  0.2 μMexon 13 detectable NO: 16] oligonucleotide BRAF wild-type PNAGCTACAGTGAAATCTCG [SEQ ID NO: 12]   1 μM PCR oligo buffer 0.632 X dNTPs 0.4 mM ROX  0.0147 μM Tacpold 11 Units MgCl₂  4 mM *F = 5-Propynyl dC,L = 5-Propynyl dU **Concentration in reaction of 25 μl target and 25 μlPCR reagents

PCR cycling included one cycle at 92° C. for 10 minutes (TaqGoldactivation) and 55 cycles (the number of cycles can be modified withoutimpacting assay performance) of 88° C./5 seconds, 92° C./15 seconds, 67°C./5 seconds, and 63° C./35 seconds (DNA amplification and fluorescencereadings). Alternatively, PCR cycling can include one cycle at 92° C.for 10 minutes (TaqGold activation) and 55 cycles of 92° C. for 15seconds, and 65° C. for 35 seconds (DNA amplification and fluorescencereadings).

Other mutations can be detected in the same manner. Allele-specificprimers can be designed for other mutations in the same manner asdescribed above for V600E/K/D SNPs. In this regard, the pooled reactioncan detect one or more of V600E, V600K and/or V600D in combination withone or more other mutations.

Example 3

This example describes alternative forward primers and detectableoligonucleotides for use in the methods.

TABLE 5 Alternative Primers and Detectable oligonucleotides Mutationdetected at V600 of Oligonucleotide Sequence and Label (5′→3′and N→C for PNA) BRAF BRAF Forward primerAATAGGTGATTTTGGTCTAGCTACAAA [SEQ ID NO: 22] E, K, D, R, N FPd MU2BRAF Forward primer AATAGGTGATTTTGGTCTAGCTACCGA [SEQ ID NO: 23] E, DFpd MU3 BRAF Forward primer AATAGGTGATTTTGGTCTAGCTACGGA [SEQ ID NO: 24]E, D FPd MU4 BRAF Forward primerAATAGGTGATTTTGGTCTAGCTACTGAG [SEQ ID NO: 25] E MU-f1aBRAF Forward primer AATAGGTGATTTTGGTCTAGCTACGGAG [SEQ ID NO: 26] EMU-f1c BRAF Forward primer AATAGGTGATTTTGGTCTAGCTACTGAA [SEQ ID NO: 27]E MU-f2a BRAF Forward primerAATAGGTGATTTTGGTCTAGCTACGGAA [SEQ ID NO: 28] E MU-f2cBRAF Forward primer AATAGGTGATTTTGGICTAGCTACCAAG [SEQ ID NO: 29] KMU-f3b BRAF Forward primer AATAGGTGATTITGGICTAGCTACGAAG [SEQ ID NO: 30]K MU-f3c BRAF Forward primerAATAGGTGATTTTGGTCTAGCTACCAAA [SEQ ID NO: 31] K MU-f4bBRAF Forward primer AATAGGTGATTTTGGTCTAGCTACGAAA [SEQ ID NO: 32] KMU-f4c BRAF Forward primer AATAGGTGATTTTGGTCTAGCTACAAAC [SEQ ID NO: 33]K, N FPd MU9 BRAF Forward primerAATAGGTGATTTTGGTCTAGCTACAAAT [SEQ ID NO: 34] K, D, N FPd MU10BRAF Forward primer AATAGGTGATTTTGGTCTAGCTACAAC [SEQ ID NO: 35] K, R, NFPd MU11 BRAF Forward primer AATAGGTGATTTTGGTCTAGCTACGAA [SEQ ID NO: 36]K, N FPd MU12 BRAF Forward primerAATAGGTGATTTTGGTCTAGCTACCAA [SEQ ID NO: 37] K, N FPd MU13Internal Control GATCTCAGTAAGGTACGGAGTAACTGTC [SEQ ID NO: 38]exon 17 forward primer Internal ControlTAGTCTGTTCTTTTGGATAGCATGAAGCT [SEQ ID NO: 39] exon 17 reverse primerInternal Control Quasar-GALGAGAGAFFAFLFLLLFF-BHQ2-dT* [SEQ IDexon 17 detectable NO: 40] oligonucleotide Internal ControlCTAAATAAGTCTTTACACCCCCAAGTATGTTC [SEQ ID NO: exon 14 forward primer 41]Internal Control CTGTGGATGATTGACTTGGCGTGTAAG [SEQ ID NO: 42]exon 14 reverse primer Internal ControlQuasar-AGALLLFGAGGFFAGAGLFF-BHQ2-dT* [SEQ ID exon 14 detectable NO: 43]oligonucleotide *F = 5-Propynyl dC, L = 5-Propynyl dU

Example 4

This example describes reactions for detection of individual SNPs atV600 in exon 15 of the BRAF gene in mRNA.

Total nucleic acids or RNA from human FFPE tumor tissues are used as atemplate for the reverse transcription/PCR amplification reaction. Totalnucleic acids are isolated and purified from FFPE samples using apurification kit such as QIAmp FFPE DNA tissue kit (Qiagen) withoutRNase treatment. RNA can be isolated and purified from FFPE samplesusing an RNA purification kit such as RNeasy kit (Qiagen), sometimestogether with DNase treatment. For RNA detection, reverse transcriptionis initiated from a reverse primer (BRAF-R3) that anneals to a sequencewithin exon 15 of the BRAF gene. This BRAF sequence element is common toall BRAF exon 15 containing transcripts; therefore, the single reverseprimer can promote reverse transcription of all targeted variants fromRNA. PCR amplification of the resulting cDNA is directed by theabove-mentioned reverse primer in combination with multiple forwardprimers that specifically anneal to BRAF V600E, V600K, or V600Dsequences at the SNP sites. The same primers can also be used to amplifygenomic DNA containing targeted variants.

In addition to the primer/detectable oligonucleotide set that detectsV600E, V600K, or V600D from total nucleic acid or RNA, aprimer/detectable oligonucleotide set is designed to detect a sequencewithin BRAF exon 13 as internal control. The amplification levels ofBRAF exon 13 are used to normalize the BRAF variants detection processagainst variations in sample adequacy, sample extraction process, totalBRAF RNA expression level and amplification efficiency. In order toamplify both RNA and genomic DNA, BRAF internal control primer 2 isdesigned within exon 13.

The reaction formulation and cycling condition for detection from RNAand/or total nucleic acids can be same or similar to those of the V600E,V600K, or V600D reaction in the DNA SNP assay (see, e.g., Example 1),with the exceptions that the cycling condition contains a reversetranscription step prior to the normal thermal cycling program and maycontain a different enzyme. PCR reaction is set up containing theoligonucleotides as shown in Tables 6, 7, and 8.

It is sometimes desired that only RNA, not genomic DNA, is detected forBRAF V600 mutations and the internal control. To achieve that, inaddition to the RNA-specific sample preparation, the reverse primer canbe designed to be located at the adjacent exon, i.e., exon 16 for V600mutations and exon 14 for the internal control, such as within the exonor straddling an exon-exon junction. Due to the long intron sequencesbetween exons 15 and 16 and between exons 13 and 14, such PCR oligodesigns can only amplify RNA (without introns), and not genomic DNA(with introns), for both BRAF V600 mutations and internal control.

TABLE 6 V600E Reaction Oligonucleotide Sequence and label (5′→3′for DNA and N→C for PNA) BRAF V600E forward primer 1AATAGGTGATTTTGGTCTAGCTACCGAG [SEQ ID NO: 8] BRAF V600E forward primer 2AATAGGTGATTTTGGTCTAGCTACCGAA [SEQ ID NO: 9] BRAF reverse primer 2CACAAAATGGATCCAGACAACTGTTC [SEQ ID NO: 44]BRAF detectable oligonucleotideFAM-LGGAGLGGGLFFFALFAGLL-BHQ1-dT* [SEQ ID NO: 11] BRAF wild-type PNAGCTACAGTGAAATCTCG [SEQ ID NO: 12] BRAF V600K PNAGCTACAAAGAAATCTCG [SEQ ID NO: 13] Internal Control forward primerGTATCACCATCTCCATATCATTGAGACC [SEQ ID NO: 14]Internal Control reverse primerTCCATGCCCTGTGCAGTCTGTCGTG [SEQ ID NO: 45] Internal ControlQuasar-GFAFGAFAGAFLGFAFAGG-BHQ2-dT* [SEQ ID NO: 16]detectable oligonucleotide *F = 5-Propynyl dC, L = 5-Propynyl dU

TABLE 7 V600K Reaction Oligonucleotide Sequence and label (5′→3′for DNA and N→C for PNA) BRAF V600K forward primer 1AATAGGTGATTTTGGTCTAGCTACTAAG [SEQ ID NO: 17] BRAF V600K forward primer 2AATAGGTGATTTTGGTCTAGCTACTAAA [SEQ ID NO: 18] BRAF reverse primer 2CACAAAATGGATCCAGACAACTGTTC [SEQ ID NO: 44]BRAF detectable oligonucleotideFAM-LGGAGLGGGLFFFALFAGLL-BHQ1-dT* [SEQ ID NO: 11] BRAF wild-type PNAGCTACAGTGAAATCTCG [SEQ ID NO: 12] BRAF V600E PNAGCTACAGAGAAATCTCG [SEQ ID NO: 19] Internal Control forward primerGTATCACCATCTCCATATCATTGAGACC [SEQ ID NO: 14]Internal Control reverse primer 2TCCATGCCCTGTGCAGTCTGTCGTG [SEQ ID NO: 45] Internal ControlQuasar-GFAFGAFAGAFLGFAFAGG-BHQ2-dT* [SEQ ID NO: 16]detectable oligonucleotide *F = 5-Propynyl dC, L = 5-Propynyl dU

TABLE 8 V600D Reaction Oligonucleotide Sequence and label (5′→3′for DNA and N→C for PNA) BRAF V600D forward primer 1AATAGGTGATTTTGGTCTAGCTACTGAT [SEQ ID NO: 20] BRAF V600D forward primer 2AATAGGTGATTTTGGTCTAGCTACTGAC [SEQ ID NO: 21] BRAF reverse primer 2CACAAAATGGATCCAGACAACTGTTC [SEQ ID NO: 44]BRAF detectable oligonucleotideFAM-LGGAGLGGGLFFFALFAGLL-BHQ1-dT* [SEQ ID NO: 11] BRAF wild-type PNAGCTACAGTGAAATCTCG [SEQ ID NO: 12] Internal Control forward primerGTATCACCATCTCCATATCATTGAGACC [SEQ ID NO: 14]Internal Control reverse primer 2TCCATGCCCTGTGCAGTCTGTCGTG [SEQ ID NO: 45] Internal Control Quasar-GFAFGAFAGAFLGFAFAGG-BHQ2-dT* [SEQ ID NO: 16]detectable oligonucleotide

Example 5

The sequences used in this experiment are given above and in FIG. 1.FIG. 8 shows data from experiments wherein primers (the primers ofFIG. 1) were made to distinguish between wild-type BRAF, BRAF with theV600E mutation and BRAF with the V600K mutation. In the first row (rowsrun from left to right; columns run from top to bottom) the wild-type ormutant designation is given for the target sequence. Below the targetsequence designation is the nucleotide sequence for the 3′ end of thetarget sequence. The sequence is underlined and the mutant nucleotidesare in red. Below the sequence is the amino acid encoded by the givensequence.

For example, in the first block on the first row, the target sequence isnamed “WT1799a,” the nucleotide sequence is “GTG” and the sequenceencodes valine “Val(V).”

The first column of the Figure gives the 1) name of the primer and thesequence encoded by the 3′ end of the primer, 2) the number ofmismatches as compared to the target sequence, 3) the position of themismatches from the 3′ end of the subject sequence and, 4) the PCRresult given in dCt (delta Concentration of target).

Thus, the box located at column 2, row 2 can be interpreted asindicating that the primer (MUf1b) for BRAF-T1799a, has two mismatches,the mismatches are located on the second and forth nucleotide and thedCt result was 9.35 when compared to the result for using the sameprimer for its intended target, T1799a. The dCt value for using a primerfor its intended target is arbitrarily set to zero thus all results arerelative to this value.

When the boxes at row 2, columns 2 and 3 are compared, it be seen thatwhen a second mismatch is incorporated into the primer, the primer doesnot detect the wild-type target as efficiently as it does the intendedtarget, the mutant BRAF, wherein there is only one mismatchednucleotide.

The genetic code is redundant allowing one amino acid to be encoded bymore than one nucleotide trimer. In this regard, changes in a specificamino acid may be encoded by two or more different nucleotide mutations.FIG. 6 shows that primers designed to detect nucleotide mutations thatresult in the same amino acid change (e.g., V600E) do not detect thesemutations as efficiently if the primers have more than one mutationrelative to the specific target sequence as compared to primers thathave a single nucleotide mismatch. Therefore, this data shows that theinventive concept described in the specification with regard to improveddetection of SNPs is not limited to any particular sequence or intendedtarget but, rather, is a concept that is broadly applicable to theimproved detection of SNPs.

What is claimed is:
 1. A method of detecting at least one mutation (X)of the codon encoding valine at amino acid position 600 (V600X) in exon15 of the BRAF gene in a sample of nucleic acid from a human, whichmethod comprises: (a) performing an amplification reaction with thesample of nucleic acid, wherein the amplification reaction comprises aprimer, the last three nucleotides at the 3′ terminus of which encodes Xand wherein the fourth nucleotide from the 3′ terminus contains a baseother than adenine (A), wherein, if X is present, the primer anneals toX, wherein, if the sample of nucleic acid is mRNA, step (a) furthercomprises obtaining cDNA reverse-transcribed from the mRNA orreverse-transcribing cDNA from the mRNA before performing theamplification reaction, whereupon, if X is present, the amplificationreaction produces an amplification product comprising X, and (b)detecting, and optionally quantitating, the amplification productcomprising X, wherein, if X is encoded by more than one codon, theamplification reaction comprises a primer for each codon, whereupon aV600X mutation in exon 15 of the BRAF gene in a sample of nucleic acidfrom a human is detected.
 2. The method of claim 1, wherein theamplification reaction further comprises at least one peptide nucleicacid (PNA) clamp, wherein at least one PNA clamp blocks theamplification from wild-type target, and wherein, if the amplificationreaction comprises one or more other PNA clamps, the PNA clamps adetectable oligonucleotide and/or a primer by binding an unwanted targetand preventing a primer from amplifying from an unwanted target.
 3. Themethod of claim 1, wherein detecting the amplification productcomprising X comprises detecting a labeled primer or contacting theamplification product with a detectable oligonucleotide and detectinghybridization of the detectable oligonucleotide to the amplificationproduct comprising X.
 4. The method of claim 1, wherein theamplification reaction further comprises an internal control primer, inwhich case the amplification reaction also produces an amplificationproduct comprising the internal control, in which case step (b) includesdetecting the amplification product comprising the internal control. 5.The method of claim 4, wherein detecting the amplification productcomprising the internal control comprises detecting a labeled primer orcontacting the amplification product with a detectable oligonucleotideand detecting hybridization of the detectable oligonucleotide to theamplification product comprising the internal control.
 6. The method ofclaim 1, wherein X is at least one amino acid selected from the groupconsisting of E, K, D R, and N.
 7. The method of claim 1, wherein X isat least one amino acid selected from the group consisting of E, K, andD.
 8. The method of claim 1, wherein X is E.
 9. The method of claim 1,wherein X is E and K, E and D, or K and D.
 10. The method of claim 1,wherein X is E, K, and D.
 11. The method of claim 1, wherein, when themethod comprises detecting two or more X, the method can compriseperforming an amplification reaction with the sample of DNA for each Xtogether or separately.
 12. The method of claim 11, wherein the methodfurther comprises determining which X is present in the sample of DNA.13-25. (canceled)
 26. A method of detecting at least one mutation (X) ofa codon in a gene in a sample of nucleic acid, which method comprises:(a) performing an amplification reaction with the sample of nucleicacid, wherein the amplification reaction comprises a primer, the lastthree nucleotides at the 3′ terminus of which encodes X and wherein thefourth nucleotide from the 3′ terminus contains a base other thanadenine (A), wherein, if X is present, the primer anneals to X, wherein,if the sample of nucleic acid is mRNA, step (a) further comprisesobtaining cDNA reverse-transcribed from the mRNA or reverse-transcribingcDNA from the mRNA before performing the amplification reaction,whereupon, if X is present, the amplification reaction produces anamplification product comprising X, (b) detecting the amplificationproduct comprising X, and wherein, if X is encoded by more than onecodon, the amplification reaction comprises a primer for each codon,whereupon a mutation is detected in the codon of the gene in a sample ofnucleic acid from a human is detected.
 27. The method of claim 26,wherein the amplification reaction further comprises at least one PNAclamp, wherein at least one PNA clamp blocks the amplification fromwild-type target, and wherein, if the amplification reaction comprisesone or more other PNA clamps, the PNA clamps a detectableoligonucleotide and/or a primer by binding an unwanted target andpreventing a primer from amplifying from an unwanted target. the PNAclamps a detectable oligonucleotide and/or a primer.
 28. The method ofclaim 26, wherein detecting the amplification product comprising Xcomprises detecting a labeled primer or contacting the amplificationproduct with a detectable oligonucleotide and detecting hybridization ofthe detectable oligonucleotide to the amplification product comprisingX.
 29. The method of claim 26, wherein the amplification reactionfurther comprises an internal control primer, in which case theamplification reaction also produces an amplification product comprisingthe internal control, in which case step (b) includes detecting theamplification product comprising the internal control.
 30. The method ofclaim 29, wherein detecting the amplification product comprising theinternal control comprises detecting a labeled primer or contacting theamplification product with a detectable oligonucleotide and detectinghybridization of the detectable oligonucleotide to the amplificationproduct comprising the internal control.
 31. The method of claim 29,wherein, when the method comprises detecting two or more X, the methodcan comprise performing an amplification reaction with the sample of DNAfor each X together or separately.
 32. A method of designing a primerfor detection of at least one mutation (X) of a codon in a gene in asample of nucleic acid, which method comprises synthesizing a primer,the last three nucleotides at the 3′ terminus of which encodes X andwherein the fourth nucleotide from the 3′ terminus contains a base otherthan that which is present in the wild-type gene, whereupon a primer fordetection of at least one mutation (X) in a codon in a gene in a sampleof nucleic acid is designed.